## ----echo = FALSE, message = FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ options(width = 750) knitr::opts_chunk$set( comment = "#>", error = FALSE, tidy = FALSE) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # length(listGenomes(db = "refseq")) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # length(listGenomes(db = "genbank")) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # length(listGenomes(db = "ensembl")) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # the number of genomes available for each kingdom # listKingdoms(db = "refseq") ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # the number of genomes available for each kingdom # listKingdoms(db = "genbank") ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # the number of genomes available for each kingdom # listKingdoms(db = "ensembl") ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # the number of genomes available for each group # listGroups(db = "refseq") ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # the number of genomes available for each group # listGroups(db = "genbank") ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # download the genome of Homo sapiens from refseq # # and store the corresponding genome file in '_ncbi_downloads/genomes' # HS.genome.refseq <- getGenome( db = "refseq", # organism = "Homo sapiens", # path = file.path("_ncbi_downloads","genomes") ) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # download the genome of Homo sapiens from refseq # # and store the corresponding genome file in '_ncbi_downloads/genomes' # HS.genome.refseq <- getGenome( db = "refseq", # organism = "Homo sapiens") ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # import downloaded genome as Biostrings object # Human_Genome <- read_genome(file = HS.genome.refseq) # ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # look at the Biostrings object # Human_Genome ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # install.packages("magrittr") # library(magrittr) # # import genome as Biostrings object # Human_Genome <- getGenome( db = "refseq", # organism = "Homo sapiens", # path = file.path("_ncbi_downloads","genomes")) %>% # read_genome() ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # Human_Genome ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # install.packages("magrittr") # library(magrittr) # # import genome as Biostrings object # Scerevisiae_Genome <- getGenome( # db = "refseq", # organism = "559292") %>% # read_genome() ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # Scerevisiae_Genome ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # install.packages("magrittr") # library(magrittr) # # import genome as Biostrings object # Scerevisiae_Genome <- getGenome( # db = "refseq", # organism = "GCF_000146045.2") %>% # read_genome() ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # Scerevisiae_Genome ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # download the genome of Homo sapiens from Genbank # # and store the corresponding genome file in '_ncbi_downloads/genomes' # HS.genome.genbank <- getGenome( db = "genbank", # organism = "Homo sapiens", # path = file.path("_ncbi_downloads","genomes") ) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # import downloaded genome as Biostrings object # Human_Genome <- read_genome(file = HS.genome.genbank) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # look at the Biostrings object # Human_Genome ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # install.packages("magrittr") # library(magrittr) # # import genome as Biostrings object # Scerevisiae_Genome <- getGenome( # db = "genbank", # organism = "559292") %>% # read_genome() ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # Scerevisiae_Genome ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # install.packages("magrittr") # library(magrittr) # # import genome as Biostrings object # Scerevisiae_Genome <- getGenome( # db = "genbank", # organism = "GCA_000146045.2") %>% # read_genome() ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # Scerevisiae_Genome ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # download the genome of Homo sapiens from ENSEMBL # # and store the corresponding genome file in '_ncbi_downloads/genomes' # HS.genome.ensembl <- getGenome( db = "ensembl", # organism = "Homo sapiens", # path = file.path("_ncbi_downloads","genomes") , # assembly_type = "primary_assembly") ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # import downloaded genome as Biostrings object # Human_Genome <- read_genome(file = HS.genome.ensembl) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # look at the Biostrings object # Human_Genome ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # install.packages("magrittr") # library(magrittr) # # import genome as Biostrings object # Scerevisiae_Genome <- getGenome( # db = "ensembl", # organism = "4932") %>% # read_genome() ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # Scerevisiae_Genome ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # install.packages("magrittr") # library(magrittr) # # import genome as Biostrings object # Scerevisiae_Genome <- getGenome( # db = "ensembl", # organism = "GCA_000146045.2") %>% # read_genome() ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # Scerevisiae_Genome ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # download the proteome of Homo sapiens from refseq # # and store the corresponding proteome file in '_ncbi_downloads/proteomes' # HS.proteome.refseq <- getProteome( db = "refseq", # organism = "Homo sapiens", # path = file.path("_ncbi_downloads","proteomes")) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # import proteome as Biostrings object # Human_Proteome <- read_proteome(file = HS.proteome.refseq) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # Human_Proteome ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # install.packages("magrittr") # library(magrittr) # # import proteome as Biostrings object # Human_Proteome <- getProteome( db = "refseq", # organism = "Homo sapiens", # path = file.path("_ncbi_downloads","proteomes")) %>% # read_proteome() ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # Human_Proteome ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # download the proteome of Homo sapiens from genbank # # and store the corresponding proteome file in '_ncbi_downloads/proteomes' # HS.proteome.genbank <- getProteome( db = "genbank", # organism = "Homo sapiens", # path = file.path("_ncbi_downloads","proteomes")) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # import proteome as Biostrings object # Human_Proteome <- read_proteome(file = HS.proteome.genbank) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # Human_Proteome ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # download the proteome of Homo sapiens from ENSEMBL # # and store the corresponding proteome file in '_ncbi_downloads/proteomes' # HS.proteome.ensembl <- getProteome( db = "ensembl", # organism = "Homo sapiens", # path = file.path("_ncbi_downloads","proteomes")) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # import proteome as Biostrings object # Human_Proteome <- read_proteome(file = HS.proteome.ensembl) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # Human_Proteome ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # download the proteome of Mus musculus from UniProt # # and store the corresponding proteome file in '_uniprot_downloads/proteomes' # Mm.proteome.uniprot<- getProteome( db = "uniprot", # organism = "Mus musculus", # path = file.path("_uniprot_downloads","proteomes")) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # import proteome as Biostrings object # Mouse_Proteome <- read_proteome(file = Mm.proteome.uniprot) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # Mouse_Proteome ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # download the genome of Homo sapiens from refseq # # and store the corresponding genome CDS file in '_ncbi_downloads/CDS' # HS.cds.refseq <- getCDS( db = "refseq", # organism = "Homo sapiens", # path = file.path("_ncbi_downloads","CDS")) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # import downloaded CDS as Biostrings object # Human_CDS <- read_cds(file = HS.cds.refseq, # obj.type = "Biostrings") # ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # look at the Biostrings object # Human_CDS ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # install.packages("magrittr") # library(magrittr) # # import CDS as Biostrings object # Human_CDS <- getCDS( db = "refseq", # organism = "Homo sapiens", # path = file.path("_ncbi_downloads","CDS")) %>% # read_cds(obj.type = "Biostrings") ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # Human_CDS ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # download the genome of Homo sapiens from genbank # # and store the corresponding genome CDS file in '_ncbi_downloads/CDS' # HS.cds.genbank <- getCDS( db = "genbank", # organism = "Homo sapiens", # path = file.path("_ncbi_downloads","CDS")) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # import downloaded CDS as Biostrings object # Human_CDS <- read_cds(file = HS.cds.genbank, # obj.type = "Biostrings") # ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # look at the Biostrings object # Human_CDS ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # download the genome of Homo sapiens from ensembl # # and store the corresponding genome CDS file in '_ncbi_downloads/CDS' # HS.cds.ensembl <- getCDS( db = "ensembl", # organism = "Homo sapiens", # path = file.path("_ncbi_downloads","CDS")) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # import downloaded CDS as Biostrings object # Human_CDS <- read_cds(file = HS.cds.ensembl, # obj.type = "Biostrings") # ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # look at the Biostrings object # Human_CDS ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # download the RNA of Homo sapiens from refseq # # and store the corresponding RNA file in '_ncbi_downloads/RNA' # HS.rna.refseq <- getRNA( db = "refseq", # organism = "Homo sapiens", # path = file.path("_ncbi_downloads","RNA")) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # import downloaded RNA as Biostrings object # Human_rna <- read_rna(file = HS.rna.refseq, # obj.type = "Biostrings") # ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # look at the Biostrings object # Human_rna ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # install.packages("magrittr") # library(magrittr) # # import RNA as Biostrings object # Human_rna <- getRNA( db = "refseq", # organism = "Homo sapiens", # path = file.path("_ncbi_downloads","RNA")) %>% # read_cds(obj.type = "Biostrings") ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # Human_rna ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # download the RNA of Homo sapiens from genbank # # and store the corresponding genome RNA file in '_ncbi_downloads/RNA' # HS.rna.genbank <- getRNA( db = "genbank", # organism = "Homo sapiens", # path = file.path("_ncbi_downloads","RNA")) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # import downloaded RNA as Biostrings object # Human_rna <- read_cds(file = HS.rna.genbank, # obj.type = "Biostrings") # ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # look at the Biostrings object # Human_rna ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # download the RNA of Homo sapiens from ensembl # # and store the corresponding genome RNA file in '_ncbi_downloads/RNA' # HS.rna.ensembl <- getRNA( db = "ensembl", # organism = "Homo sapiens", # path = file.path("_ncbi_downloads","RNA")) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # import downloaded RNA as Biostrings object # Human_rna <- read_cds(file = HS.rna.ensembl, # obj.type = "Biostrings") # ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # look at the Biostrings object # Human_rna ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # download the GFF file of Homo sapiens from refseq # # and store the corresponding file in '_ncbi_downloads/annotation' # HS.gff.refseq <- getGFF( db = "refseq", # organism = "Homo sapiens", # path = file.path("_ncbi_downloads","annotation")) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # import downloaded GFF file # Human_GFF <- read_gff(file = HS.gff.refseq) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # Human_GFF ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # download the GFF file of Homo sapiens from genbank # # and store the corresponding file in '_ncbi_downloads/annotation' # HS.gff.genbank <- getGFF( db = "genbank", # organism = "Homo sapiens", # path = file.path("_ncbi_downloads","annotation")) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # import downloaded GFF file # Human_GFF <- read_gff(file = HS.gff.genbank) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # show all elements of the data.frame # # options(tibble.print_max = Inf) # Human_GFF ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # download the GFF file of Homo sapiens from ENSEMBL # # and store the corresponding file in 'ensembl/annotation' # HS.gff.ensembl <- getGFF( db = "ensembl", # organism = "Homo sapiens", # path = file.path("ensembl","annotation")) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # import downloaded GFF file # Human_GFF <- read_gff(file = HS.gff.ensembl) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # show all elements of the data.frame # # options(tibble.print_max = Inf) # Human_GFF ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # download the GTF file of Homo sapiens from ENSEMBL # # and store the corresponding file in 'ensembl/annotation' # HS.gtf.ensembl <- getGTF( db = "ensembl", # organism = "Homo sapiens", # path = file.path("ensembl","annotation"), # assembly_type = "primary_assembly") ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # download repeat masker annotation file for Homo sapiens # Hsapiens_rm <- getRepeatMasker( db = "refseq", # organism = "Homo sapiens", # path = file.path("refseq","TEannotation")) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # import TE annotation file # Hsapiens_rm_import <- read_rm("refseq/TEannotation/Homo_sapiens_rm_refseq.out.gz") # # look at data # Hsapiens_rm_import ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # download genome assembly stats file for Homo sapiens # Hsapiens_stats <- getAssemblyStats( db = "refseq", # organism = "Homo sapiens", # path = file.path("refseq","AssemblyStats")) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # import TE annotation file # Hsapiens_stats_import <- read_assemblystats(Hsapiens_stats) # # look at data # Hsapiens_stats_import ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # download genome assembly stats file for Homo sapiens # Hsapiens_stats <- getAssemblyStats( db = "genbank", # organism = "Homo sapiens", # path = file.path("genbank","AssemblyStats")) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # import TE annotation file # Hsapiens_stats_import <- read_assemblystats(Hsapiens_stats) # # look at data # Hsapiens_stats_import ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # # download collection for Saccharomyces cerevisiae # getCollection( db = "refseq", # organism = "Saccharomyces cerevisiae", # path = file.path("refseq","Collections"))