plotDispEsts: Plot dispersion estimates

In aghozlane/DESeq2shaman: Differential gene expression analysis based on the negative binomial distribution

Description

A simple helper function that plots the per-gene dispersion estimates together with the fitted mean-dispersion relationship.

Usage

## S4 method for signature 'DESeqDataSet'
plotDispEsts(object, ymin,
  genecol = "black", fitcol = "red", finalcol = "dodgerblue",
  legend=TRUE, xlab, ylab, log = "xy", cex = 0.45, ...)

## S4 method for signature 'DESeqDataSet'
plotDispEsts(object, ymin, genecol = "black",
  fitcol = "red", finalcol = "dodgerblue", legend = TRUE, xlab, ylab,
  log = "xy", cex = 0.45, ...)

Arguments

object	a DESeqDataSet
ymin	the lower bound for points on the plot, points beyond this are drawn as triangles at ymin
genecol	the color for gene-wise dispersion estimates
fitcol	the color of the fitted estimates
finalcol	the color of the final estimates used for testing
legend	logical, whether to draw a legend
xlab	xlab
ylab	ylab
log	log
cex	cex
...	further arguments to plot

Author(s)

Simon Anders

Examples

dds <- makeExampleDESeqDataSet()
dds <- estimateSizeFactors(dds)
dds <- estimateDispersions(dds)
plotDispEsts(dds)

aghozlane/DESeq2shaman documentation built on Nov. 1, 2019, 9:01 p.m.