plotSparsity {DESeq2} | R Documentation

## 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

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

[Package DESeq2 version 1.20.0 Index]