totalCounts: Get the total counts

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

View source: R/totalCounts.R

Description

Get the total number of read pairs in a set of Hi-C libraries.

Usage

1

Arguments

files

a character vector containing paths to the index files generated from each Hi-C library

param

a pairParam object containing read extraction parameters

Details

As the name suggests, this function counts the total number of read pairs in each index file prepared by preparePairs. Use of param$fragments ensures that the chromosome names in each index file are consistent with those in the desired genome (e.g., from cutGenome). Counting will also consider the values of restrict, discard and cap in param.

Value

An integer vector is returned containing the total number of read pairs in each library.

Author(s)

Aaron Lun

See Also

preparePairs, cutGenome, pairParam, squareCounts

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)

# Setting up the parameters
fout <- tempfile(fileext=".h5")
invisible(preparePairs(hic.file, param, file=fout))

# Counting totals, and comparing them.
totalCounts(fout, param)
squareCounts(fout, param, width=10)$totals

new.param <- reform(param, restrict="chrA")
totalCounts(fout, new.param)
squareCounts(fout, new.param, width=10)$totals

new.param <- reform(param, discard=GRanges("chrA", IRanges(1, 50)))
totalCounts(fout, new.param)
squareCounts(fout, new.param, width=10)$totals

new.param <- reform(param, cap=1)
totalCounts(fout, new.param)
squareCounts(fout, new.param, width=10)$totals

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