prcfq: Process fastq file

In shkonishi/rsko: This is my personal package of R functions

Process fastq file

Description

Process fastq file and create a data.frame of quality score

Usage

prcfqs(file, n)

prcfqlen(file)

prcfqbox(file, n, ...)

prcfq2box(file1, file2, n, col2, ...)

prcfq2den(file1, file2, col2, lab)

prcfqlen(file)

prcfqbox(file, n, ...)

prcfq2box(file1, file2, n, col2, ...)

prcfq2den(file1, file2, col2, lab)

Arguments

file	<CHAR> input file path
n	<INT> Size of sampling [default: 10000]　 　If a negative value is selected, all reads are used.
...	additional plot options [required for 'boxplot' ]
file1, file2	<CHAR> input file path
col2	<CHAR>|<NUM> character or numeric (vector), the border color of the boxplot.
lab	<CHAR>

Examples

## Not run: 
#
 in_f1 <- "test_R1.fq.bz2"
 in_f2 <- "test_R2.fq.bz2"
 res <- prcfqs(in_f1)
 cols <- adjustcolor(c(1,2), 0.5)

 prcfqbox(file = in_f1, n = 10000)
 prcfq2box(file1 = in_f1, file2 = in_f2, n = 10000, col2 = cols)
 prcfq2den(file1 = in_f1, file2 = in_f2, col2 = cols)


## End(Not run)

shkonishi/rsko documentation built on Feb. 21, 2023, 5:12 a.m.