maprate: Parse hisat2 log file

Description Usage Arguments Value Examples

View source: R/maprate.R

Description

Parse hisat2 log file and extract mapping rate of all samples.

Usage

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maprate(fp, lab, pair, algnr)

Arguments

fp

file path of bowtie log

lab

character: file name as sample name.

pair

logical: paired end read or nod. The default value is TRUE.

algnr

character: select an alignr from 'hisat2' or 'bowtie2'. The default value is "bowtie2".

Value

data frame of mapping rate and ggplot object

Examples

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h2.paired.log <- system.file("extdata", "hisat2_log.txt", package = "rskoseq")
label <- c("A","B","C","D")
res <- maprate(fp = h2.paired.log, lab = label)

shkonishi/rskoseq documentation built on Oct. 30, 2018, 1:10 p.m.