pqHists: P- and q-value distributions plotted side-by-side

In jtlovell/RNAseqDE: A pipeline for differential expression analyses in R

Description

pqHists Make histograms of p-value and q-value distributions

Usage

pqHists(x, what.p = "p.value", what.q = "q.value", alpha = 0.05,
  main = "significance distribution", ...)

Arguments

x	matrix containing p-values and q-values
what.p	the name of the column containing p-values
what.q	the name of the column containing q-values
main	The stem of the title, to which significance counts are attached
...	additional arguments passed on to hist, like the color of the bars

Examples

## Not run: 
data(kidney) # from simseq package
counts<-kidney$counts
counts<-counts[sample(1:nrow(counts),1000),]
info<-data.frame(rep=kidney$replic, treatment=kidney$treatment)
stats<-pipeLIMMA(counts=counts, info=info, formula = " ~ treatment", block=NULL)
stats.fullmodel<-stats$stats
pqHists(stats.fullmodel, what.p="ebayesPvalue_treatmentTumor",
   what.q="ebayesQvalue_treatmentTumor",
   main="main effect treatment", breaks=100)

## End(Not run)

jtlovell/RNAseqDE documentation built on May 10, 2019, 8:06 a.m.