pairReads: Function pairs aligned paired NGS reads
In GOTHiC: Binomial test for Hi-C data analysis

Description Usage Arguments Value Author(s) See Also Examples

View source: R/GOTHiC.R

This function takes bowtie output files, pairs the reads, only keeps those where both ends mapped, filters for perfect duplicates to avoid PCR bias, and saves and returns a GenomicRangesList object that contains the paired_reads_1 and paired_reads_2 GenomicRanges with the paired reads

1 2	pairReads(fileName1, fileName2, sampleName, DUPLICATETHRESHOLD = 1, fileType='BAM')

`fileName1`	File containing the mapped reads of the first fragment ends (BAM or Bowtie format)
`fileName2`	File containing the mapped reads of the second fragment ends (BAM or Bowtie format)
`sampleName`	A character string that will be used to name the exported BedGraph file containing the coverage, and the R object file with paired reads. They will be saved in the current directory.
`DUPLICATETHRESHOLD`	An integer specifying the maximum amount of duplicated paired-end reads allowed, over that value it is expected to be PCR bias. The default is 1.
`fileType`	A character string specifying the format of the aligned reads. The default is 'BAM'. Other accepted format is 'Bowtie'.

A GenomicRangesList called filtered

`paired_reads_1`	GenomicRanges with the coordinates of where one end of the read mapped
`paired_reads_2`	GenomicRanges with the coordinates of where the other end of the read mapped

Borbala Mifsud and Robert Sugar

mapReadsToRestrictionSites, GOTHiC

library(GOTHiC)
dirPath <- system.file("extdata", package="HiCDataLymphoblast")
fileName1 <- list.files(dirPath, full.names=TRUE)[1]
fileName2 <- list.files(dirPath, full.names=TRUE)[2]
paired <- pairReads(fileName1, fileName2, sampleName='lymphoid_chr20', 
DUPLICATETHRESHOLD = 1, fileType='Table')