plotDifftoBase: Plot absolute log2 fold-change against base mean of...

In ABSSeq: ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences

Description

Plot absolute differencs against expression levels

Usage

plotDifftoBase(object, foldname = "foldChange", adj.pcut = 0.05,
  cols = c("black", "red"), pch = 16, xlab = "log2 of Expression level",
  ylab = "log2 fold-change", ...)

Arguments

object	a ABSDataSet
foldname	indicates kind of fold-change in plotting, default is 'foldChange', see results
adj.pcut	cutoff for differential expressed genes, marked by different color, default is 0.05
cols	the colors to mark the non-DE and DE genes, defualt is black and red, respectively
pch	pch, default is 16
xlab	xlab, default is 'log2 of Expression level'
ylab	ylab, default is 'log2 fold-change'
...,	further arguments to plot

Details

Plot absolute differencs against expression levels and mark the gene with a color at a given cutoff of fold-change

Examples

data(simuN5)
obj <- ABSDataSet(counts=simuN5$counts, groups=factor(simuN5$groups))
obj <- ABSSeq(obj)
plotDifftoBase(obj)

Example output

eistimating size factors....
calculating parameters and fitting....
Normalizing used qtotal!
Calling p-value and adjusted it....

ABSSeq documentation built on Nov. 8, 2020, 5:07 p.m.