topTags {edgeR} | R Documentation |
Displays/Returns the top DE tags in a data frame
topTags(object,n=10,adj.method= "BH")
object |
deDGEList , output from deDGE |
n |
number of tags to display/return |
adj.method |
method used to adjust P-values, using p.adjust |
Data frame containing the relative level of expression, log fold changes, unadjusted and adjusted P-values
Mark Robinson
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.
# 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)