mergePairs: Merge read pairs

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/mergePairs.R

Description

Merge index files for multiple Hi-C libraries into a single output file.

Usage

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mergePairs(files, file.out)

Arguments

files

a character vector containing the paths to the index files to be merged

file.out

a character string specifying the path to the output index file

Details

Hi-C libraries are often split into technical replicates. This function facilitates the merging of said replicates into a single library for downstream processing. Index files listed in files should be produced by preparePairs, with or without pruning by prunePairs.

Value

A merged index file is produced at the specified location. A NULL object is invisibly returned.

Author(s)

Aaron Lun

See Also

preparePairs, prunePairs

Examples

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hic.file <- system.file("exdata", "hic_sort.bam", package="diffHic")
cuts <-readRDS(system.file("exdata", "cuts.rds", package="diffHic"))
param <- pairParam(cuts)

fout <- tempfile(fileext=".h5")
fout2 <- tempfile(fileext=".h5")
fout3 <- tempfile(fileext=".h5")
invisible(preparePairs(hic.file, param, fout))
invisible(prunePairs(fout, param, fout2))
invisible(prunePairs(fout, param, fout3, max.frag=50))

# Note: don't save to a temporary file for actual data.
mout <- tempfile(fileext=".h5")
mergePairs(c(fout2, fout3), mout)

require(rhdf5)
h5read(fout2, "chrA/chrA")
h5read(fout3, "chrA/chrA")
h5read(mout, "chrA/chrA")

diffHic documentation built on April 29, 2020, 2:08 a.m.