mergePairs {diffHic} | R Documentation |
Merge index files for multiple Hi-C libraries into a single output file.
mergePairs(files, file.out)
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 |
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
.
A merged index file is produced at the specified location.
A NULL
object is invisibly returned.
Aaron Lun
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")