| Version: | 1.0 |
| Date: | 2025-05-05 |
| Title: | Random GO Database |
| Maintainer: | Barry Zeeberg <barryz2013@gmail.com> |
| Author: | Barry Zeeberg [aut, cre] |
| Depends: | R (≥ 4.2.0) |
| Imports: | minimalistGODB, GO.db, graphics, stats |
| Description: | The Gene Ontology (GO) Consortium https://geneontology.org/ organizes genes into hierarchical categories based on biological process (BP), molecular function (MF) and cellular component (CC, i.e., subcellular localization). Tools such as 'GoMiner' (see Zeeberg, B.R., Feng, W., Wang, G. et al. (2003) <doi:10.1186/gb-2003-4-4-r28>) can leverage GO to perform ontological analysis of microarray and proteomics studies, typically generating a list of significant functional categories. The significance is traditionally determined by randomizing the input gene list to computing the false discovery rate (FDR) of the enrichment p-value for each category. We explore here the novel alternative of randomizing the GO database rather than the gene list. |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| Encoding: | UTF-8 |
| VignetteBuilder: | knitr |
| Suggests: | knitr, rmarkdown, testthat (≥ 3.0.0) |
| RoxygenNote: | 7.3.2 |
| Config/testthat/edition: | 3 |
| NeedsCompilation: | no |
| Packaged: | 2025-05-05 22:57:13 UTC; barryzeeberg |
| Repository: | CRAN |
| Date/Publication: | 2025-05-07 12:10:02 UTC |
DBstats
Description
display some gene and category stats
Usage
DBstats(DB, title = NULL, ontology = "biological_process", verbose = TRUE)
Arguments
DB |
GOGOA3 or a randomized version of it |
title |
character if not null, title for output |
ontology |
character c("biological_process","molecular_function","cellular_component") |
verbose |
Boolean if TRUE print out some information |
Value
returns no values, but prints out some stats
Examples
## Not run:
# GOGOA3.RData is too large to include in the R package
# so I need to load it from a file that is not in the package.
# Since this is in a file in my own file system, I could not
# include this as a regular example in the package.
# This example is given in full detail in the package vignette.
# You can generate GOGOA3.RData using the package 'minimalistGODB'
# or you can retrieve it from https://github.com/barryzee/GO/databases
dir<-"/Users/barryzeeberg/personal/GODB_RDATA/goa_human/"
load(sprintf("%s/%s",dir,"GOGOA3_goa_human.RData"))
DBstats(GOGOA3,ontology="biological_process")
## End(Not run)
addName2List
Description
add the leaf category name to the list of ancestor categories
Usage
addName2List(GOBPANCESTOR)
Arguments
GOBPANCESTOR |
GO.db data set |
Value
returns an augmented list of ancestor categories
Examples
BP_ANCESTOR<-addName2List(as.list(GO.db::GOBPANCESTOR))
characterizeDB
Description
compute distribution of GO category sizes, and fraction of a leaf's ancestors containing a bait gene
Usage
characterizeDB(
GOGOA3,
ontology = "biological_process",
ngene = 2,
GOBPCHILDREN,
GOBPANCESTOR,
hitters = "all",
verbose = TRUE
)
Arguments
GOGOA3 |
return value of minimalistGODB::buildGODatabase() |
ontology |
character c("biological_process","molecular_function","cellular_component") |
ngene |
integer number of genes to examine within range of 'hitters' |
GOBPCHILDREN |
GO.db data set |
GOBPANCESTOR |
GO.db data set |
hitters |
character c("big","mid","lo","all") designate which portion of gene table to look at |
verbose |
BOOLEAN if TRUE print out some information |
Value
returns the sorted number of GO category sizes, and also has side effect of printing out some information
Examples
## Not run:
# GOGOA3.RData is too large to include in the R package
# so I need to load it from a file that is not in the package.
# Since this is in a file in my own file system, I could not
# include this as a regular example in the package.
# This example is given in full detail in the package vignette.
# You can generate GOGOA3.RData using the package 'minimalistGODB'
# or you can retrieve it from https://github.com/barryzee/GO/databases
dir<-"/Users/barryzeeberg/personal/GODB_RDATA/goa_human/"
load(sprintf("%s/%s",dir,"GOGOA3_goa_human.RData"))
ontology<-"biological_process"
t<-characterizeDB(GOGOA3,ontology,ngene=3,GO.db::GOBPCHILDREN,GO.db::GOBPANCESTOR,hitters="all")
## End(Not run)
compare2DB
Description
compare pairs of GO_HGNC in 2 databases
Usage
compare2DB(GOGOA3, GOGOA3R, verbose = TRUE)
Arguments
GOGOA3 |
return value of minimalistGODB::buildGODatabase() |
GOGOA3R |
a supposedly randomized version of GOGOA3 |
verbose |
Boolean if TRUE print out some information |
Value
returns no values, but has side effect of printing information
Examples
## Not run:
# GOGOA3.RData is too large to include in the R package
# so I need to load it from a file that is not in the package.
# Since this is in a file in my own file system, I could not
# include this as a regular example in the package.
# This example is given in full detail in the package vignette.
# You can generate GOGOA3.RData using the package 'minimalistGODB'
# or you can retrieve it from https://github.com/barryzee/GO/databases
dir<-"/Users/barryzeeberg/personal/GODB_RDATA/goa_human/"
load(sprintf("%s/%s",dir,"GOGOA3_goa_human.RData"))
GOGOA3R<-randomGODB(GOGOA3)
compare2DB(GOGOA3,GOGOA3R)
## End(Not run)
fractAncest
Description
analysis of fraction of ancestor categories to which a leaf gene maps
Usage
fractAncest(
genes,
GOGOA3,
ontology = "biological_process",
GOBPCHILDREN,
GOBPANCESTOR,
verbose = TRUE
)
Arguments
genes |
character vector list of gene names |
GOGOA3 |
return value of minimalistGODB::buildGODatabase() |
ontology |
character c("biological_process","molecular_function","cellular_component") |
GOBPCHILDREN |
GO.db data set |
GOBPANCESTOR |
GO.db data set |
verbose |
Boolean if TRUE print out some information |
Value
returns no values, but has side effect of printing out some results
Examples
## Not run:
# GOGOA3.RData is too large to include in the R package
# so I need to load it from a file that is not in the package.
# Since this is in a file in my own file system, I could not
# include this as a regular example in the package.
# This example is given in full detail in the package vignette.
# You can generate GOGOA3.RData using the package 'minimalistGODB'
# or you can retrieve it from https://github.com/barryzee/GO/databases
dir<-"/Users/barryzeeberg/personal/GODB_RDATA/goa_human/"
load(sprintf("%s/%s",dir,"GOGOA3_goa_human.RData"))
ontology<-"biological_process"
genes<-c("CDC45","CELF2")
fractAncest(genes,GOGOA3,ontology,GO.db::GOBPCHILDREN,GO.db::GOBPANCESTOR)
## End(Not run)
geneListDistHitters
Description
compute number of GOGOA3 mappings for genes in geneList
Usage
geneListDistHitters(geneList, GOGOA3, ontologies = NULL, verbose = TRUE)
Arguments
geneList |
character vector listg of gene names |
GOGOA3 |
return value of minimalistGODB::buildGODatabase() |
ontologies |
character c("biological_process","molecular_function","cellular_component") |
verbose |
Boolean if TRUE print out some information |
Value
returns no value, but has side effect of printing information
Examples
## Not run:
# GOGOA3.RData is too large to include in the R package
# so I need to load it from a file that is not in the package.
# Since this is in a file in my own file system, I could not
# include this as a regular example in the package.
# This example is given in full detail in the package vignette.
# You can generate GOGOA3.RData using the package 'minimalistGODB'
# or you can retrieve it from https://github.com/barryzee/GO/databases
dir<-"/Users/barryzeeberg/personal/GODB_RDATA/goa_human/"
load(sprintf("%s/%s",dir,"GOGOA3_goa_human.RData"))
geneList<-GOGOA3$ontologies[["biological_process"]][1:10,"HGNC"]
geneListDistHitters(geneList,GOGOA3)
## End(Not run)
hitters
Description
pick genes of a size range and submit to fractAncest()
Usage
hitters(
GOGOA3,
ontology,
hitters,
ngene,
GOBPCHILDREN,
GOBPANCESTOR,
verbose = TRUE
)
Arguments
GOGOA3 |
return value of minimalistGODB::buildGODatabase() |
ontology |
character c("biological_process","molecular_function","cellular_component") |
hitters |
character c("big","mid","lo","all") designate which portion of gene table to look at |
ngene |
integer number of genes to examine within range of 'hitters' |
GOBPCHILDREN |
GO.db data set |
GOBPANCESTOR |
GO.db data set |
verbose |
Boolean if TRUE print out some information |
Value
returns no values, but has side effect of printing out some information
Examples
## Not run:
# GOGOA3.RData is too large to include in the R package
# so I need to load it from a file that is not in the package.
# Since this is in a file in my own file system, I could not
# include this as a regular example in the package.
# This example is given in full detail in the package vignette.
# You can generate GOGOA3.RData using the package 'minimalistGODB'
# or you can retrieve it from https://github.com/barryzee/GO/databases
dir<-"/Users/barryzeeberg/personal/GODB_RDATA/goa_human/"
load(sprintf("%s/%s",dir,"GOGOA3_goa_human.RData"))
hitters(GOGOA3,ontology="biological_process",hitters="all",
5,GO.db::GOBPCHILDREN,GO.db::GOBPANCESTOR)
## End(Not run)
leafList
Description
retrieve leaf nodes
Usage
leafList(GOBPCHILDREN)
Arguments
GOBPCHILDREN |
GO.db dataset |
Value
returns a list of leaf nodes
Examples
BP_LEAF<-leafList(GO.db::GOBPCHILDREN)
mapPerGene
Description
characterize number of mappings per gene
Usage
mapPerGene(GOGOA3, ontology, verbose = TRUE)
Arguments
GOGOA3 |
return value of minimalistGODB::buildGODatabase() |
ontology |
character c("biological_process","molecular_function","cellular_component") |
verbose |
Boolean if TRUE print out some information |
Value
returns no values, but has side effect of printing out information
Examples
## Not run:
# GOGOA3.RData is too large to include in the R package
# so I need to load it from a file that is not in the package.
# Since this is in a file in my own file system, I could not
# include this as a regular example in the package.
# This example is given in full detail in the package vignette.
# You can generate GOGOA3.RData using the package 'minimalistGODB'
# or you can retrieve it from https://github.com/barryzee/GO/databases
dir<-"/Users/barryzeeberg/personal/GODB_RDATA/goa_human/"
load(sprintf("%s/%s",dir,"GOGOA3_goa_human.RData"))
mapPerGene(GOGOA3,ontology="biological_process")
## End(Not run)
postProcess
Description
adds secondary components to database like GOGOA3$genes etc
Usage
postProcess(l)
Arguments
l |
return value of randomGODB2() |
Value
returns a database like GOGOA3
Examples
## Not run:
# GOGOA3.RData is too large to include in the R package
# so I need to load it from a file that is not in the package.
# Since this is in a file in my own file system, I could not
# include this as a regular example in the package.
# This example is given in full detail in the package vignette.
# You can generate GOGOA3.RData using the package 'minimalistGODB'
# or you can retrieve it from https://github.com/barryzee/GO/databases
dir<-"/Users/barryzeeberg/personal/GODB_RDATA/goa_human/"
load(sprintf("%s/%s",dir,"GOGOA3_goa_human.RData"))
pp<-postProcess(randomGODB(GOGOA3))
## End(Not run)
randomGODB
Description
driver to construct a randomized version of GOGOA3
Usage
randomGODB(GOGOA3, verbose = TRUE)
Arguments
GOGOA3 |
return value of minimalistGODB::buildGODatabase() |
verbose |
Boolean if TRUE print out some information |
Details
The results of characterizeDB() show that a gene mapping to a leaf node maps to only around 10% of the ancestors. So I do not need to use a more sophisticated method to generate a random database. That is, I do not need to maintain a consistency between leaf and ancestor mappings. Therefore a very simple randomization
simply scrambling the genes in an ontology of GOGOA3 will suffice.
Value
description
Examples
## Not run:
# GOGOA3.RData is too large to include in the R package
# so I need to load it from a file that is not in the package.
# Since this is in a file in my own file system, I could not
# include this as a regular example in the package.
# This example is given in full detail in the package vignette.
# You can generate GOGOA3.RData using the package 'minimalistGODB'
# or you can retrieve it from https://github.com/barryzee/GO/databases
dir<-"/Users/barryzeeberg/personal/GODB_RDATA/goa_human/"
load(sprintf("%s/%s",dir,"GOGOA3_goa_human.RData"))
GOGOA3R<-randomGODB(GOGOA3)
## End(Not run)
sizeGOcats
Description
characterize size of GO categories
Usage
sizeGOcats(GOGOA3, ontology, verbose = TRUE)
Arguments
GOGOA3 |
return value of minimalistGODB::buildGODatabase() |
ontology |
character c("biological_process","molecular_function","cellular_component") |
verbose |
Boolean if TRUE print out some information |
Value
returns no values, but has side effect of printing out information
Examples
## Not run:
# GOGOA3.RData is too large to include in the R package
# so I need to load it from a file that is not in the package.
# Since this is in a file in my own file system, I could not
# include this as a regular example in the package.
# This example is given in full detail in the package vignette.
# You can generate GOGOA3.RData using the package 'minimalistGODB'
# or you can retrieve it from https://github.com/barryzee/GO/databases
dir<-"/Users/barryzeeberg/personal/GODB_RDATA/goa_human/"
load(sprintf("%s/%s",dir,"GOGOA3_goa_human.RData"))
sizeGOcats(GOGOA3,ontology="biological_process")
## End(Not run)