Description Usage Arguments Examples

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.

1 | ```
plotSparsity(x, normalized = TRUE, ...)
``` |

`x` |
a matrix or DESeqDataSet |

`normalized` |
whether to normalize the counts from a DESeqDataSEt |

`...` |
passed to |

1 2 3 | ```
dds <- makeExampleDESeqDataSet(n=1000,m=4,dispMeanRel=function(x) .5)
dds <- estimateSizeFactors(dds)
plotSparsity(dds)
``` |

DESeq2 documentation built on Feb. 22, 2021, 10 a.m.

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