gg_qa: Quality assesment with ShortRead package and return ggplot...

In shkonishi/rskoseq: This is my personal package of R functions for NGS data

Description

This functions returns ggplot objects and create report of qa. The qa report is created at above of the fastq directory.

Usage

gg_qa(fqdir, suffix, prefix, qareport, facet_col, outdir, ow)

Arguments

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.

Value

The list of ggplot objects returns and write.table for quality assesment with 'qa'.

Examples

## 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)

shkonishi/rskoseq documentation built on April 18, 2021, 3:50 p.m.