topTags {edgeR}R Documentation

Displays the top differentially expressed tags in a table

Description

Displays/Returns the top DE tags in a data frame

Usage

 
topTags(object,n=10,adj.method= "BH")

Arguments

object deDGEList, output from deDGE
n number of tags to display/return
adj.method method used to adjust P-values, using p.adjust

Value

Data frame containing the relative level of expression, log fold changes, unadjusted and adjusted P-values

Author(s)

Mark Robinson

References

Robinson MD, Smyth GK. 'Small-sample estimation of negative binomial dispersion, with applications to SAGE data.' Biostatistics. 2008 Apr;9(2):321-32.

Robinson MD, Smyth GK. 'Moderated statistical tests for assessing differences in tag abundance.' Bioinformatics. 2007 Nov 1;23(21):2881-7.

Examples

# generate raw data from NB, create list object
y<-matrix(rnbinom(80,size=1,mu=10),nrow=20)
d<-DGEList(data=y,group=rep(1:2,each=2),lib.size=rep(c(1000:1001),2))
rownames(d$data)<-paste("tagno",1:nrow(d$data),sep=".")

# find alpha and call main procedure to find differences
alpha<-alpha.approxeb(d)
ms<-deDGE(d,alpha=alpha$alpha)

# look at top 10
topTags(ms)

[Package edgeR version 1.0.4 Index]