mergePairs {diffHic} | R Documentation

## Merge read pairs

### Description

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

### Usage

    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

    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")

[Package diffHic version 1.19.0 Index]