getSummary,.FastqcFile-method {ngsReports} | R Documentation

## Get the summary information from Fastqc Files

### Description

Read the information from the `summary.txt` files in each .FastqcFile

### Usage

    ## S4 method for signature '.FastqcFile'
    getSummary(object)

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

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

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

### Arguments

`object` | Can be a `FastqcData`, `FastqcDataList` object or a vector of paths to unparsed FastQC reports.

### Details

This simply extracts the summary of PASS/WARN/FAIL status for every module as defined by the tool FastQC for each supplied file.

### Value

A `tibble` containing the PASS/WARN/FAIL status for each module, as defined in a FastQC report.

### 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)

    # Return a tibble/tibble with the raw information
    getSummary(fdl)

[Package ngsReports version 1.0.1 Index]