fastqcWrap: Provides wrappers to FastQC from within R

Description Usage Arguments Details Value Author(s) See Also

Look through a batch of .zip files produced by FASTQC to obtain summary information across a range of files

1	fastqcSummary(fqNames, qcDir)

`fqNames`	the filenames to extract the totals for.
`qcDir`	the directory to look in for the FASTQC reports
`fqName`	the filename to extract the totals for. This should be the name of a single fastq file.
`main`	the title of the plot. Will be automatically generated if missing. Use `main = c()` to remove the plot title
`xLabLen`	the number of characters used for the labels on the x axis. Can be used to shorten long filenames.
`showGuide`	show the guide to PASS, FAIL, WARN. Defaults to FALSE
`...`	passed to `element_text()` for `axis.text.x` only

This will look in a number of .zip files, as produced by FASTQC, and will extract the PASS/FAIL/WARN information across the key report sections.

fastqcSummary will return the PASS/FAIL/WARN information for any number of FASTQC reports.

fastqcSummaryPlot will plot the output from the function fastqcSummary using default parameters. This function relies on ggplot2 using pre-defined parameters. Only the parameters for the x-axis labels (i.e. the file names) can be tweaked via the ellipsis.

the PASS/FAIL summary information from the FASTQC report(s) either as a data.frame (fastqcSummary) or as a plot (fastqcSummaryPlot)

Steve Pederson <stephen.pederson@adelaide.edu.au>

fastqc

steveped/fastqcWrap documentation built on May 30, 2019, 5:39 p.m.