gc_read: GC content per read

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

Description

This functions returns ggplot objects of GC content per read

Usage

gc_read(fqdir, outdir, suffix, prefix, facet_col)

Arguments

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.

Value

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

Examples

## 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)

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