calc_adapter_content {qckitfastq}R Documentation

Compute adapter content in reads. This function is only available for macOS/Linux.

Description

Compute adapter content in reads. This function is only available for macOS/Linux.

Usage

calc_adapter_content(infile, adapters)

Arguments

infile

filepath to fastq sequence

adapters

filepath to adapters

Value

map object with adapter names as the key and the number of times the adapters appears in the reads as the value

Examples

if(.Platform$OS.type != "windows") {
adapter_file <- system.file("extdata", "adapters.txt", package = "qckitfastq")
infile <- system.file("extdata", "test.fq.gz", package = "qckitfastq")
content <- calc_adapter_content(infile, adapter_file)
}

[Package qckitfastq version 1.8.0 Index]