readKmer: Extract the Kmer information from fastqc reports
In steveped/fastqcWrap: Provides wrappers to FastQC from within R

Description Usage Arguments Details Value Author(s)

Look through the .zip file produced by FASTQC to obtain the k-mer information

1	readKmer(fqName, qcDir, maxWidth = 25)

`fqName`	the filename to extract the totals for. This should be the name of a single fastq file.
`qcDir`	the directory to look in for the FASTQC reports
`maxWidth`	the maximum combined length of k-mers to retain, starting from the 5' end. Any k-mers which extend beyond this value will be ignored

This will look in a .zip file, as produced by FASTQC, and will extract information about over-represented k-mers This is primarily designed to explore k-mers at the 5' end of reads. Designed to return the k-mer information from a single report only.

A list with components $summary and $status

The component summary contains a data.frame with columns corresponding to the original report. It should be noted that beyond position 10 of the read, fastqc reports only give a range of bases. These are denoted in the additional column maxShift, indicating the k-mer may need to be shifted when generating a consensus sequence. This should be assessed manually.

The additional column Proportion indicates the proportion of reads containing the k-mer

The component $status returns the PASS/FAIL/WARN status

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

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