geneid.cummeRbund: Test data of significant differentially expressed genes used...

In meshr: Tools for conducting enrichment analysis of MeSH

Description

This RNA-Seq data were taken from three samples, "iPS", "hESC", and "Fibroblasts". We first create two objects of gene sets, i.e., selected and universal genes, by comparing significantly regulated genes between iPS and hESC under the significance level of 0.05 by getSig method in cummeRbund package. 303 genes were finally choosed and 104 of them were differentially expressed.

Usage

data(geneid.cummeRbund)

Source

http://www.bioconductor.org/packages/release/bioc/vignettes/cummeRbund/inst/doc/cummeRbund-manual.pdf

See Also

sig.geneid.cummeRbund.

Examples

data(geneid.cummeRbund)
names(geneid.cummeRbund)

## This data is also available by following scripts.
if(interactive()){
library(cummeRbund)
library(org.Hs.eg.db)
cuff <- readCufflinks(dir = system.file("extdata", package = "cummeRbund"))

gene.symbols <- annotation(genes(cuff))[,4]
mySigGeneIds <- getSig(cuff,x='hESC',y='iPS',alpha=0.05,level='genes')
mySigGenes <- getGenes(cuff,mySigGeneIds)

sig.gene.symbols <- annotation(mySigGenes)[,4]
gene.symbols <- gene.symbols[!is.na(gene.symbols)]
sig.gene.symbols <- sig.gene.symbols[!is.na(sig.gene.symbols)]

geneid.cummeRbund <- select(org.Hs.eg.db, keys=gene.symbols, keytype="SYMBOL", columns="ENTREZID")
sig.geneid.cummeRbund <- select(org.Hs.eg.db, keys=sig.gene.symbols, keytype="SYMBOL", columns="ENTREZID")

na.index1 <- which(is.na(geneid.cummeRbund[,2]))
for (i in na.index1){
s <- unlist(strsplit(as.character(geneid.cummeRbund[i,][1]), ","))[1]
sym <- get(s, org.Hs.egALIAS2EG)[1]
geneid.cummeRbund[i,2] <- as.integer(sym)
}

na.index2 <- which(is.na(sig.geneid.cummeRbund[,2]))
for (i in na.index2){
	s <- unlist(strsplit(as.character(sig.geneid.cummeRbund[i,][1]), ","))[1]
	sym <- get(s, org.Hs.egALIAS2EG)[1]
	sig.geneid.cummeRbund[i,2] <- as.integer(sym)
}

geneid.cummeRbund <- geneid.cummeRbund[!duplicated(geneid.cummeRbund[,2]), ]
sig.geneid.cummeRbund <- sig.geneid.cummeRbund[!duplicated(sig.geneid.cummeRbund[,2]), ]
}

meshr documentation built on Nov. 8, 2020, 6:47 p.m.