Description Usage Arguments Value Examples
This functions returns ggplot objects of GC content per read
1 | gc_read(fqdir, outdir, suffix, prefix, facet_col)
|
fqdir |
character: The file path of fastq files, or dir path, containing fastq files |
outdir |
output directory |
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. |
facet_col |
facet of sequence content and quality score per sample plot. |
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 12 | ## Not run:
# arguments
fqdir <- system.file("extdata/E-MTAB-1147", package = "ShortRead")
suffix <- ".fastq.gz"
outdir <- "~/pub/sampledata/rnaseq/project1/qa"
# execution
res_qa <- rskoseq::gc_read(fqdir, outdir, suffix, facet_col=2)
do.call(gridExtra::grid.arrange, c(res_qa, list(ncol=2)))
## End(Not run)
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