fastqc: A wrapper for the bash shell command fastqc.
In steveped/fastqcWrap: Provides wrappers to FastQC from within R

Description Usage Arguments Details Value Author(s) See Also

Takes fastq files then runs FASTQC on them

1	fastqc(files, outDir, threads = floor(detectCores()/2), args = c(), exec)

`files`	The `fastq`, `sam` or `bam` files to perform `fastqc` on. Must be specified with the complete path
`outDir`	the output directory for writing the trimmed fastq file. The names wil be automatically the same as the original file
`threads`	the number of threads to use for the process. This will be auto-detected on a Linux system & will default to half of the found number of cores.
`args`	any remaining arguments to the function `fastqc`. See the list available by typing `fastqc -h` into a terminal
`exec`	The path to the executable. If not specified this will be automatically detected.

This is a simple wrapper function for controlling & running fastqc from within R. This can be very useful for controlling & documenting an entire pipeline from within knitr to produce a simple report

The output components $fqcFiles & $outDir can be passed directly to the functions fqcSummary and fqcSummaryPlot as the appropriate arguments.

A list with the components $complete, fqcFiles, $outDir, version, command.

The component $complete is the complete message as output by fastqc, in order of completion The component $fqcFiles is the edited message from above, sorted in lexicographical order.

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

cat, system

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