plotQuality-methods {EDASeq} | R Documentation

## Methods for Function `plotQuality` in Package EDASeq

### Description

`plotQuality` produces a plot of the quality of the reads.

### Methods

`signature(x = "BamFileList")`

  It produces a plot that summarizes the per-base mean quality of the reads of each BAM file in `x`.

`signature(x = "BamFile")`

  It produces a boxplot of the per-base distribution of the quality scores of the reads in `x`.

`signature(x = "FastqFileList")`

  It produces a plot that summarizes the per-base mean quality of the reads of each FASTQ file in `x`.

### Details

Since FASTQ files can be very long, it can be very expensive to process a whole file. One way to avoid this, is to consider a subset of the file and then plot the quality of the subset. As long as one assumes that the subset is random, this is a good approximation. The function `FastqSampler` of `ShortRead` can be used for this. See its help page for an example.

[Package EDASeq version 2.20.0 Index]