maxAdapterContent: Get the maximum Adapter Content

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

Get the maximum Adapter Content

Description

Get the maximum Adapter Content across one or more FASTQC reports

Usage

maxAdapterContent(x, asPercent = TRUE)

Arguments

x	Can be a .FastqcFile, FastqcData, FastqcDataList or path
asPercent	logical. Format the values as percentages with the added ⁠\%⁠ symbol

Details

This will extract the Adapter_Content module from the supplied object, and provide a tibble with the final value for each file.

Value

A tibble object containing the percent of reads with each adapter type at the final position

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)

# Get the maxAdapterContent
maxAdapterContent(fdl)

steveped/ngsReports documentation built on July 24, 2024, 10:45 a.m.