maprate: Parse hisat2 or bowtie2 log file
In shkonishi/rskoseq: This is my personal package of R functions for NGS data

Description Usage Arguments Value Examples

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

1	maprate(fp, lab, pair, algnr)

`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".

data frame of mapping rate and ggplot object

h2.paired.log <- system.file("extdata", "hisat2_log.txt", package = "rskoseq")
label <- c("A","B","C","D")
res1 <- maprate(fp = h2.paired.log, lab = label)
res2 <- maprate(fp = h2.paired.log, pair = T, lab = label, algnr = "hisat2")