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

Description Usage Source See Also Examples

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

1

Source

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

See Also

geneid.cummeRbund.

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
data(sig.geneid.cummeRbund)
names(sig.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 May 6, 2019, 2:23 a.m.