plotQualityProfile: Plot quality profile of a fastq file.

In benjjneb/dada2: Accurate, high-resolution sample inference from amplicon sequencing data

Plot quality profile of a fastq file.

Description

This function plots a visual summary of the distribution of quality scores as a function of sequence position for the input fastq file(s).

Usage

plotQualityProfile(fl, n = 5e+05, aggregate = FALSE)

Arguments

fl	(Required). character. File path(s) to fastq or fastq.gz file(s).
n	(Optional). Default 500,000. The number of records to sample from the fastq file.
aggregate	(Optional). Default FALSE. If TRUE, compute an aggregate quality profile for all fastq files provided.

Details

The distribution of quality scores at each position is shown as a grey-scale heat map, with dark colors corresponding to higher frequency. The plotted lines show positional summary statistics: green is the mean, orange is the median, and the dashed orange lines are the 25th and 75th quantiles.

If the sequences vary in length, a red line will be plotted showing the percentage of reads that extend to at least that position.

Value

A ggplot2 object. Will be rendered to default device if printed, or can be stored and further modified. See ggsave for additional options.

Examples

plotQualityProfile(system.file("extdata", "sam1F.fastq.gz", package="dada2"))

benjjneb/dada2 documentation built on Feb. 1, 2024, 10:50 p.m.