Description Usage Arguments Value Examples
This functions returns ggplot objects and create report of qa. The qa report is created at above of the fastq directory.
1 | gg_qa(fqdir, suffix, prefix, qareport, facet_col, outdir, ow)
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fqdir |
A vector of file path of fastq files, or dir path, containing fastq files |
suffix |
A pattern of fastq file suffix. The default is ".fastq.gz" |
prefix |
A vector of samples name. The default values are names of fastq files containing in fqdir, which substitute 'suffix' character. |
qareport |
logical. reporting or not. The default value is FALSE. |
facet_col |
integer. facet of sequence content and quality score per sample plot. |
outdir |
output directory. The default values is same at fqdir. |
ow |
logical. It must be TRUE if overwritten. The default value is FALSE. |
The list of ggplot objects returns and write.table for quality assesment with 'qa'.
1 2 3 4 5 6 7 8 9 10 11 | ## Not run:
# arguments
p <- system.file("extdata/E-MTAB-1147", package = "ShortRead")
sffx <- ".fastq.gz"
prfx <- sub(sffx,"",list.files(p, sffx))
# execution
res_qa <- rskoseq::gg_qa(fqdir=p, suffix=sffx, prefix=prfx, facet_col=2)
do.call(gridExtra::grid.arrange, c(res_qa, list(ncol=2)))
## End(Not run)
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