plotQualityProfile: Plot quality profile of a fastq file.

Description Usage Arguments Details Value Examples

View source: R/plot-methods.R

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

1

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.

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

1
plotQualityProfile(system.file("extdata", "sam1F.fastq.gz", package="dada2"))

dada2 documentation built on Nov. 17, 2017, 10:21 a.m.