dot-FastqcFile-class: The .FastqcFile Object Class

Description Arguments Details Value Slots Examples

Description

The .FastqcFile Object Class defines a path to the output from the standalone tool FastQC. \lifecyclestable

Arguments

x

character(1) denoting a file.path

Details

This class simply refers to a fastqc output file after checking for existence and validity (i.e. the correct internal structure). Underlying files can be zipped (*_fastqc.zip) or extracted directories

The helper function .FastqcFile() is a simple constructor which checks validity and enables construction of other dependent classes.

Value

An object of class .FastqcFile

Slots

path

Character vector of length 1 which contains a valid file path.

Examples

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# Get the files included with the package
packageDir <- system.file("extdata", package = "ngsReports")
fl <- list.files(packageDir, pattern = "fastqc.zip", full.names = TRUE)[1]

# As this is the root structure, we can only call this
# function with an individual file
ff <- ngsReports:::.FastqcFile(fl)

UofABioinformaticsHub/fastqcReports documentation built on Nov. 21, 2020, 7:44 p.m.