Return the Underlying Fastq File Names from Fastqc/Fastp Objects

fqName(object)

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

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

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

fqName(object) <- value

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

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

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

# S4 method for class '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)
#> [1] "ATTG_R1.fastq" "ATTG_R2.fastq" "CCGC_R1.fastq" "CCGC_R2.fastq"
#> [5] "GACC_R1.fastq" "GACC_R2.fastq"

nm <- paste0(letters[seq_along(fdl)], ".fq")
fqName(fdl) <- nm
fqName(fdl)
#> [1] "a.fq" "b.fq" "c.fq" "d.fq" "e.fq" "f.fq"