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
plotQualityProfile(fl, n = 5e+05)

Arguments

fl

(Required). character. File path(s) to fastq or fastq.gz file(s).

n

(Optional). Default 1,000,000. The number of records to sample from the fastq file.

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

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

dada2 documentation built on May 31, 2017, 10:56 a.m.