plotSparsity: Sparsity plot

In nlhuong/ZeroInflatedDESeq2: Differential gene expression analysis based on the negative binomial distribution

Description

A simple plot of the concentration of counts in a single sample over the sum of counts per gene. Not technically the same as "sparsity", but this plot is useful diagnostic for datasets which might not fit a negative binomial assumption: genes with many zeros and individual very large counts are difficult to model with the negative binomial distribution.

Usage

plotSparsity(x, normalized = TRUE, ...)

Arguments

x	a matrix or DESeqDataSet
normalized	whether to normalize the counts from a DESeqDataSEt
...	passed to plot

Examples

dds <- makeExampleDESeqDataSet(n=1000,m=4,dispMeanRel=function(x) .5)
dds <- estimateSizeFactors(dds)
plotSparsity(dds)

nlhuong/ZeroInflatedDESeq2 documentation built on May 23, 2019, 9:06 p.m.