extractFastqcAdpContents: Extract FastQC

In timflutre/rutilsfastqc: Utilitary functions to handle output from FastQC

Description

Returns the adapter content along the sequences per entry in a set of zip archives generated by FastQC. To be used after readFastqcZips(). When reads are long, FastQC can average adapter content over a given range, e.g. over two successive bases, such as "11-12". In such a case, because the ranges can be different for different fastq files in all.qc, this function will set adapter content to the first base of the range in the ouput, here "11", the other, here "12", will get NA.

Usage

extractFastqcAdpContents(all.qc, adp = "Illumina Universal Adapter")

Arguments

all.qc	return value from readFastqcZips()
adp	name of the adapter to plot (default="Illumina Universal Adapter")

Value

numeric matrix with entries in rows and positions along sequences in columns

Author(s)

Timothee Flutre [cre,aut], Nicolas Rode [ctb]

timflutre/rutilsfastqc documentation built on May 31, 2019, 2:16 p.m.