Test data of significant differentially expressed genes used in cummeRbund package.

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]), ]
}

Results

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)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

> library(meshr)
Loading required package: fdrtool
Loading required package: Category
Loading required package: stats4
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

Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

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: cummeRbund
Loading required package: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Loading required package: reshape2
Loading required package: fastcluster

Attaching package: 'fastcluster'

The following object is masked from 'package:stats':

    hclust

Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Gviz
Loading required package: grid

Attaching package: 'cummeRbund'

The following object is masked from 'package:GenomicRanges':

    promoters

The following object is masked from 'package:IRanges':

    promoters

The following object is masked from 'package:Biobase':

    samples

The following object is masked from 'package:BiocGenerics':

    conditions

Loading required package: org.Hs.eg.db

Loading required package: MeSH.db
Loading required package: MeSHDbi

Attaching package: 'MeSHDbi'

The following object is masked from 'package:utils':

    packageName

Loading required package: MeSH.AOR.db
Loading required package: MeSH.PCR.db
Loading required package: MeSH.Hsa.eg.db
Loading required package: MeSH.Aca.eg.db
Loading required package: MeSH.Bsu.168.eg.db
Loading required package: MeSH.Syn.eg.db
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/meshr/geneid.cummeRbund.Rd_%03d_medium.png", width=480, height=480)
> ### Name: geneid.cummeRbund
> ### Title: Test data of significant differentially expressed genes used in
> ###   cummeRbund package.
> ### Aliases: geneid.cummeRbund
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(geneid.cummeRbund)
> names(geneid.cummeRbund)
[1] "SYMBOL"   "ENTREZID"
> 
> ## 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)
Getting gene information:
	FPKM
	Differential Expression Data
	Annotation Data
	Replicate FPKMs
	Counts
Getting isoforms information:
	FPKM
	Differential Expression Data
	Annotation Data
	Replicate FPKMs
	Counts
Getting CDS information:
	FPKM
	Differential Expression Data
	Annotation Data
	Replicate FPKMs
	Counts
Getting TSS information:
	FPKM
	Differential Expression Data
	Annotation Data
	Replicate FPKMs
	Counts
Getting promoter information:
	distData
Getting splicing information:
	distData
Getting relCDS information:
	distData
> 
> 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")
'select()' returned many:1 mapping between keys and columns
> sig.geneid.cummeRbund <- select(org.Hs.eg.db, keys=sig.gene.symbols, keytype="SYMBOL", columns="ENTREZID")
'select()' returned 1:1 mapping between keys and columns
> 
> 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)
+ }
Error in .checkKeys(value, Rkeys(x), x@ifnotfound) : 
  value for "PRAMEF16" not found
Calls: get ... keys<- -> keys<- -> Rkeys<- -> Rkeys<- -> .checkKeys
Execution halted