The directed acyclic graph (DAG) based on finding the most specific
terms for the supplied Entrez Gene IDs is constructed and returned. The
constructuion is per GO ontology (there are three, MF, BP and CC) and
once the most specific terms have been identified then all less
specific terms are found (these are the parents of the terms) and then
their parents and so on, until the root is encountered.
A logical value indicating whether the GO root node
should be removed or not.
mapfun
A function taking a character vector of Entrez Gene IDs
as its only argument and returning a list of "GO lists" matching the
structure of the lists in the GO maps of annotation data packages.
The function should behave similarly to
mget(x, eg2gomap, ifnotfound=NA),
that is, NA should be returned if a specified Entrez ID has
no GO mapping. See details for the interaction of mapfun and
chip.
chip
The name of a DB-based annotation data package (the name
will end in ".db"). This package will be used to generate an Entrez
ID to GO ID mapping instead of mapfun.
Details
For each supplied Entrez Gene identifier all the GO annotations (in the
specified ontology) are found. The mapping is achieved in one of
three ways:
If mapfun is provided, it will be used to perform the
needed lookups. In this case, chip will be ignored.
If chip is provided and mapfun=NULL, then the
needed lookups will be done based on the Entrez to GO mappings
encapsulated in the specified annotation data package. This is
the recommended usage.
If mapfun and chip are NULL or missing,
then the function will attempt to load the GO package (the
environment-based package, distinct from GO.db). This package
contains a legacy environment mapping Entrez IDs to GO IDs. If
the GO package is not available, an error will be raised.
Omitting both mapfun and chip is not recommended as
it is not compatible with the DB-based annotation data packages.
The mappings are different for the different ontologies. Typically a
GO indentifier is used only in one specific ontology.
The resulting structure is stored in a graph using the graph
package, again from Bioconductor.
Value
An object that inherits from the graph class. The particular
implementation is not specified.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(GOstats)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: Category
Loading required package: stats4
Loading required package: AnnotationDbi
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: Matrix
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
Loading required package: graph
Attaching package: 'GOstats'
The following object is masked from 'package:AnnotationDbi':
makeGOGraph
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GOstats/makeGOGraph.Rd_%03d_medium.png", width=480, height=480)
> ### Name: makeGOGraph
> ### Title: Construct a GO Graph
> ### Aliases: makeGOGraph
> ### Keywords: manip
>
> ### ** Examples
>
> library("hgu95av2.db")
Loading required package: org.Hs.eg.db
> set.seed(321)
> gN <- unique(sample(keys(hgu95av2.db, 'ENTREZID'), 4))
> gg1 <- makeGOGraph(gN, "BP", chip="hgu95av2.db")
>
>
>
>
>
>
> dev.off()
null device
1
>