checkPairedEnd: Test whether a bam file if single end or paired end

Description Usage Arguments Value Examples

View source: R/checkPairedEnd.R

Description

Check the first 100000 first reads of the bam file to see whether it is single end or paired end

Usage

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checkPairedEnd(file, yieldSize = 1e+05)

Arguments

file

the input bam file. Your bamfile should be sorted and have an index file located at the same path as well.

yieldSize

the number of reads to be checked, 100000 by default.

Value

return TRUE if the input file is paired end, and FALSE if it is single end

Examples

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file <- system.file('extdata','s1.sorted.bam',package = 'strandCheckR')
checkPairedEnd(file)

strandCheckR documentation built on Nov. 1, 2018, 2:26 a.m.