marginCounts: Collect marginal counts for each bin

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

View source: R/marginCounts.R

Description

Count the number of read pairs mapped to each bin across multiple Hi-C libraries.

Usage

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marginCounts(files, param, width=50000, restrict.regions=FALSE)

Arguments

files

a character vector containing paths to the index files

param

a pairParam object containing read extraction parameters

width

an integer scalar specifying the width of each bin

restrict.regions

A logical scalar indicating whether the output regions should be limited to entries in param$restrict.

Details

The genome is first split into non-overlapping adjacent bins of size width, which are rounded to the nearest restriction site. The marginal count for each bin is defined as the number of reads in the library mapped to the bin. This acts as a proxy for genomic coverage by treating Hi-C data as single-end.

Each row of the output RangedSummarizedExperiment refers to a single bin in the linear genome, instead of a bin pair in the interaction space. The count matrix for all row can be extracted using the assay method. Bin coordinates can be extracted using the rowRanges method.

Larger marginal counts can be collected by increasing the width value. However, this comes at the cost of spatial resolution as adjacent events in the same bin can no longer be distinguished.

Note that no filtering is performed to remove empty bins. This is meant to make it easier to match up results with the output of squareCounts, as anchor IDs are directly comparable. If restrict.regions=TRUE, only counts for bins in chromosomes in param$fragments are returned.

Counting will consider the values of restrict, discard and cap in param. See pairParam for more details.

Value

A RangedSummarizedExperiment object containing the marginal counts for each bin.

Author(s)

Aaron Lun

See Also

squareCounts, RangedSummarizedExperiment-class

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(fragments=cuts)

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

# Collating to count combinations.
mar <- marginCounts(fout, param, width=10)
head(assay(mar))
mar <- marginCounts(fout, param, width=50)
head(assay(mar))
mar <- marginCounts(fout, param, width=100)
head(assay(mar))

# Attempting with other parameters.
mar <- marginCounts(fout, reform(param, restrict="chrA"), width=50)
head(assay(mar))
mar <- marginCounts(fout, reform(param, cap=1), width=50)
head(assay(mar))
mar <- marginCounts(fout, reform(param, discard=GRanges("chrA", IRanges(1, 50))), width=50)
head(assay(mar))

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