getSummary: Get the summary information from Fastqc Files

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

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)

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