plot_overrep_kmer: Create a box plot of the log2(observed/expected) ratio across...

In compbiocore/qckitfastq: FASTQ Quality Control

Description

Create a box plot of the log2(observed/expected) ratio across the length of the sequence as well as top overrepresented kmers. Only ratios greater than 2 are included in the box plot. Default is 20 bins across the length of the sequence and the top 2 overrepresented kmers, but this can be changed by the user.

Usage

plot_overrep_kmer(overkm, bins = 20, top_num = 2, output_file = NA)

Arguments

overkm	data frame with columns pos, obsexp_ratio, and kmer
bins	number of intervals across the length of the sequence
top_num	number of most overrepresented kmers to plot
output_file	File to write plot to. Will not write to file if NA. Default NA.

Value

A box plot of the log2(observed/expected ratio) across the length of the sequence

Examples

infile <- system.file("extdata", "test.fq.gz",
    package = "qckitfastq")
over_km <- overrep_kmer(infile,k=4)
plot_overrep_kmer(over_km)

compbiocore/qckitfastq documentation built on Sept. 20, 2019, 9:30 a.m.