DESeq2 (version 1.12.3)

plotSparsity: Sparsity plot

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

Run this code

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

Run the code above in your browser using DataCamp Workspace