.FastqcFile-class {ngsReports} | R Documentation

## The .FastqcFile Object Class

### Description

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

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

### 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

### Value

An object of class .FastqcFile

### Slots

`path`

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

### Examples

    # 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)

[Package ngsReports version 1.2.0 Index]