fqName-methods: Return the Underlying Fastq File Names from Fastqc/Fastp...

In steveped/ngsReports: Load FastqQC reports and other NGS related files

Return the Underlying Fastq File Names from Fastqc/Fastp Objects

Description

Return the Underlying Fastq File Names from Fastqc/Fastp Objects

Usage

fqName(object)

## S4 method for signature 'ANY'
fqName(object)

## S4 method for signature 'FastqcData'
fqName(object)

## S4 method for signature 'FastqcDataList'
fqName(object)

fqName(object) <- value

## S4 replacement method for signature 'FastqcData'
fqName(object) <- value

## S4 replacement method for signature 'FastqcDataList'
fqName(object) <- value

## S4 method for signature 'FastpData'
fqName(object)

## S4 method for signature 'FastpDataList'
fqName(object)

Arguments

object	An object able to extract an Fastq name from
value	Replacement value for fqName

Value

Returns the names of the Fastq files the FastQC report was generated from, without any preceding directories.

Examples

# Get the files included with the package
packageDir <- system.file("extdata", package = "ngsReports")
fl <- list.files(packageDir, pattern = "fastqc.zip", full.names = TRUE)

# Load the FASTQC data as a FastqcDataList object
fdl <- FastqcDataList(fl)
fqName(fdl)

nm <- paste0(letters[seq_along(fdl)], ".fq")
fqName(fdl) <- nm
fqName(fdl)

steveped/ngsReports documentation built on April 2, 2024, 5:10 p.m.