adapter_content: Creates a sorted from most frequent to least frequent...

In compbiocore/qckitfastq: FASTQ Quality Control

Description

Creates a sorted from most frequent to least frequent abundance table of adapters that are found to be present in the reads at greater than 0.1% of the reads. If output_file is selected then will save the entire set of adapters and counts. Only available for macOS/Linux due to dependency on C++14.

Usage

adapter_content(infile, adapter_file = system.file("extdata",
  "adapters.txt", package = "qckitfastq"), output_file = NA)

Arguments

infile	the path to a gzipped FASTQ file
adapter_file	Path to adapters.txt file. Default from package.
output_file	File to save data frame to. Default NA.

Value

Sorted table of adapters and counts.

Examples

if(.Platform$OS.type != "windows") {
infile <- system.file("extdata","test.fq.gz",
    package = "qckitfastq")
adapter_content(infile)[1:5]
}

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