plotQuality produces a plot of the quality of the reads.
signature(x = "BamFileList")
It produces a plot that summarizes the per-base mean quality of the reads of each BAM file in
signature(x = "BamFile")
It produces a boxplot of the per-base distribution of the quality scores of the reads in
signature(x = "FastqFileList")
It produces a plot that summarizes the per-base mean quality of the reads of each FASTQ file in
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
ShortRead can be used for this. See its help page for an example.