gc_read: GC content per read

Description Usage Arguments Value Examples

View source: R/gc_read.R

Description

This functions returns ggplot objects of GC content per read

Usage

1
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

1
2
3
4
5
6
7
8
## arguments
# fqdir <- system.file("extdata/E-MTAB-1147", package = "ShortRead")
# suffix <- ".fastq.gz"
# outdir <- "~/pub/sampledata/rnaseq/project1/qa"

## execution
# res_qa <- gc_read(fqdir, outdir, suffix, facet_col=2)
# do.call(gridExtra::grid.arrange, c(res_qa, list(ncol=2)))

shkonishi/rskoseq documentation built on Sept. 11, 2018, 12:39 a.m.