It creates gene set collections from a given list of gene sets
to be used
for the EGSEA analysis.
Usage
buildCustomIdxEZID(entrezIDs, gsets, anno = NULL, label = "custom",
name = "Custom", species = "Human", min.size = 1)
Arguments
entrezIDs
character, a vector that stores the Entrez Gene IDs tagged
in your dataset.
The order of the Entrez Gene IDs should match those of the count/expression
matrix row names.
gsets
list, list of gene sets. Each gene set is character vector of
Enterz IDs.
The names of the list should match the GeneSet column in the anno
argument (if it is provided).
anno
list, dataframe that stores a detailed annotation for each gene
set.
Some of its fields can be ID, GeneSet, PubMed, URLs, etc. The GeneSet field
is mandatory and
should have the same names as the gsets' names.
label
character,a unique id that identifies the collection of gene
sets
name
character,the collection name to be used in the EGSEA report
species
character, determine the organism of selected gene sets:
"human", "mouse" or "rat".
min.size
integer, the minium number of genes required in a testing
gene set
Details
It indexes newly created gene sets and attach gene set annotation
if provided.
Value
indexed gene set annotation that can be used with other functions in
the package.
Each annotation is a list of seven elements: original stores the
original gene sets,
idx stores the indexed gene sets, anno that stores detailed
annotation for each
gene set, label a unique id that identifies the collection of gene
sets,
featureIDs stores the entrezIDs used in building the annotation,
species
stores that organism name of gene sets and name stores the
collection name
to be used in the EGSEA report.
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(EGSEA)
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: gage
Loading required package: AnnotationDbi
Loading required package: stats4
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: topGO
Loading required package: graph
Loading required package: GO.db
Loading required package: SparseM
Attaching package: 'SparseM'
The following object is masked from 'package:base':
backsolve
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
Attaching package: 'topGO'
The following object is masked from 'package:IRanges':
members
The following object is masked from 'package:gage':
geneData
Loading required package: pathview
Loading required package: org.Hs.eg.db
##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.
The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
KEGG.db contains mappings based on older data because the original
resource was removed from the the public domain before the most
recent update was produced. This package should now be considered
deprecated and future versions of Bioconductor may not have it
available. Users who want more current data are encouraged to look
at the KEGGREST or reactome.db packages
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/EGSEA/buildCustomIdxEZID.Rd_%03d_medium.png", width=480, height=480)
> ### Name: buildCustomIdxEZID
> ### Title: Custom Gene Set Collection Index
> ### Aliases: buildCustomIdxEZID
>
> ### ** Examples
>
> library(EGSEAdata)
> data(il13.data)
> v = il13.data$voom
> kegg = buildIdxEZID(entrezIDs=rownames(v$E), species="human",
+ msigdb.gsets="none",
+ kegg.updated=FALSE, kegg.exclude = c("Metabolism"))
[1] "Building KEGG pathways annotation object ... "
> gsets = kegg$kegg$original[1:50]
> gs.annots = buildCustomIdxEZID(entrezIDs=rownames(v$E), gsets= gsets,
+ species="human")
[1] "Building custom pathways annotation object ... "
> names(gs.annots)
[1] "original" "idx" "anno" "label" "featureIDs"
[6] "species" "name"
>
>
>
>
>
>
>
> dev.off()
null device
1
>