| Type: | Package |
| Title: | Split Chromosome 'Fasta' File |
| Description: | Chromosome files in the 'Fasta' format usually contain large sequences like human genome. Sometimes users have to split these chromosomes into different files according to their chromosome number. The 'chromseq' can help to handle this. So the selected chromosome sequence can be used for downstream analysis like motif finding. Howard Y. Chang(2019) <doi:10.1038/s41587-019-0206-z>. |
| Version: | 0.1.3 |
| License: | Artistic-2.0 |
| Encoding: | UTF-8 |
| LazyData: | true |
| RoxygenNote: | 7.0.2 |
| NeedsCompilation: | no |
| URL: | https://github.com/MSQ-123/chromseq |
| BugReports: | https://github.com/MSQ-123/chromseq/issues |
| Depends: | R (≥ 2.10) |
| Imports: | utils, base |
| Packaged: | 2020-05-08 13:06:01 UTC; lenovo |
| Author: | Shaoqian Ma [aut, cre] |
| Maintainer: | Shaoqian Ma <897341109@qq.com> |
| Repository: | CRAN |
| Date/Publication: | 2020-05-11 15:20:17 UTC |
Sampled Fasta file of chromosome sequence from hg19 blacklist
Description
This dataset is sampled from The hg19 blacklist. For splitting a chromosome Fasta file, sometimes the Fasta identifier is too complicated to manipulate. This data can be used to show how to simplify the Fasta identifier.
Usage
data(id)
Format
A character sequence with 20 elements
References
Satpathy A T, Granja J M, Yost K E, et al. (2019) Nature biotechnology 37,925–936. (PubMed)
Examples
data(id)
Make a list file from large chromosome Fasta file
Description
Make a list file from large chromosome Fasta file
Usage
readToList(id = id, text = text, con = con)
Arguments
id |
The id list made from subFasID function |
text |
Large character read in by readLines function from Fasta file |
con |
A connection object or a character string, the connection must refer to the same Fasta file as text |
Value
Chromosome Fasta file in list format.
Examples
data("text")
id <- subFasID(text = text)
fil <- tempfile(fileext = ".data")
write(text,file = fil)
con0 <- file(fil, "r")
tex <- readToList(id,text = text,con = con0)
Replace tedious chromosome identifier into simple format
Description
Make the chromosome id starting with ">" into simple format like ">chr:1091194-1093520...",this is helpful for sorting the chromosome according to their number
Usage
replaceText(type = "text", input = input)
Arguments
type |
This can be either "text" or "list", The previous is a large character containing each line of the Fasta file, the latter is a list in which each element contains a unit of Fasta file |
input |
The large character or list containing ids that need to be simplified |
Value
The large character or list of Chromosome Fasta file with simplified id.
Author(s)
Shaoqian Ma
Examples
data("id")
simpleID<- replaceText(type = "text",input = id)
Sort the chromosome list according to the chromosome number
Description
Sort the chromosome list according to the chromosome number
Usage
sortList(id = id, tex = tex, chrsig = "single")
Arguments
id |
The identifier list of the Fasta file made by subFasID |
tex |
A chromosome Fasta file in list format made by readToList function |
chrsig |
The number of characters of the chromosome, either "single" or "double", the previous means a single character following "chr" in the Fasta identifier, the latter means two characters following "chr" in the Fasta identifier. eg."chr1,chrX,chrY,chrM" is "single";"chr10,chr11" is "double". If you want to obtain both "single" and "double" sorted list of chromosome, try "single" and "double" respectively |
Value
The sorted chromosome Fasta file in list format.
Examples
data("tex")
data("text")
text<- replaceText(type = "text",input = text)
id <- subFasID(text = text)
tex2<- sortList(id=id,tex = tex,chrsig = "single")
tex3 <- sortList(id=id,tex = tex,chrsig = "double")
Split all chromosomes from the sorted chromosome list
Description
Split all chromosomes from the sorted chromosome list
Usage
splitChr(tex = tex, chr = chr, sex = FALSE, outdir = ".")
Arguments
tex |
The sorted chromosome list made by sortList function. |
chr |
The chromosome number sequence, if the chromosome list is "single" which means a single character following "chr" in the Fasta identifier, be sure starting with 1 and ending with 9; if the chromosome list is "double" which means two characters following "chr" in the Fasta identifier, be sure that starting with 10 but the ending can be changed. |
sex |
Whether to output the sex chromosomes like X chromosome and Y chromosome. |
outdir |
The output directory. |
Value
Write the splitted chromosome Fasta file to separated txt files according to the chromosome number.
Author(s)
Shaoqian Ma
Examples
data(tex)
data(text)
#Simplify the Fasta id
text<- replaceText(type = "text",input = text)
#Subtract id
id <- subFasID(text = text)
#Sort the fasta according to the chromosome number in id
tex2<- sortList(id=id,tex = tex,chrsig = "single")
tex3 <- sortList(id=id,tex = tex,chrsig = "double")
outdir <- tempdir()
#Output the results
splitChr(tex = tex2,chr=seq(1,9),sex = TRUE,outdir = outdir)
splitChr(tex = tex3,chr=seq(10,22),sex = FALSE,outdir = outdir)
Subtract chromosome ids from Fasta file
Description
Subtract chromosome ids from Fasta file
Usage
subFasID(text = text)
Arguments
text |
Large character read by readLines from chromosome Fasta file. |
Value
The id list of the Fasta file.
Examples
data("text")
text<- replaceText(type = "text",input = text)
id <- subFasID(text = text)
Fasta file of chromosome sequence produced from sequence character
Description
Data from "Three representative inter and intra-subspecific crosses reveal the genetic architecture of reproductive isolation in rice."
Usage
data(tex)
Format
A large list containing 62 elements.
References
Li, G. et al. (2017) The Plant Journal 92, 349–362. (PubMed)
Examples
data(tex)
Fasta file of chromosome sequence
Description
A downsampled dataset containing the hg19 chromosome sequence from the hg19 blacklist. The hg19 blacklist is obtained from the supplementary dataset from "Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion." The dataset is sent to the UCSC Table Browser for obtaining the corresponding sequence file. The sequence file is processed with replaceText function to simplify the fasta id. To best illustate the usage, the sequence file is downsampled.
Usage
data(text)
Format
A character sequence with 2099 elements.
References
Satpathy A T, Granja J M, Yost K E, et al. (2019) Nature biotechnology 37, 925–936. (PubMed)
Examples
data(text)