domainDirections: Calculate domain directionality

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

View source: R/domainDirections.R

Description

Collect directionality statistics for domain identification with genomic bins.

Usage

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domainDirections(files, param, width=50000, span=10)

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

width

an integer scalar specifying the width of each bin in base pairs

span

an integer scalar specifying the distance to consider for up/downstream interactions

Details

The genome is partitioned into bins of size width. For each bin, this function computes the total number of read pairs between that bin and the span upstream bins (i.e., those with higher genomic coordinates). This is repeated for the span downstream bins, thus yielding two counts (up and down) per bin.

A RangedSummarizedExperiment is returned containing the coordinates of each bin and two matrices of counts, named "up" and "down". Each row of the matrix corresponds to a bin, while each column corresponds to a library in files. Each entry of the matrix stores the total count of read pairs to upstream or downstream bins.

The total up- and downstream counts can be used to compute a directionality statistic, e.g., as defined by Dixon et al, or by computing the log-fold change between fields. Alternatively, it can be used to identify differential domains - see the user's guide for more details.

Value

A RangedSummarizedExperiment object with one row for each bin in the genome. It contains two integer matrices named "up" and "down", containing the counts to upstream and downstream bins respectively.

Author(s)

Aaron Lun

References

Dixon JR et al. (2012). Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485:376-380.

See Also

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(fragments=cuts)

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

# Not really that informative; see user's guide.
out <- domainDirections(fout, param, width=10)
out

# Calculating directionality log-FC with a large prior.
up.counts <- assay(out, "up")
down.counts <- assay(out, "down")
dir.logFC <- log2((up.counts+10)/(down.counts+10))
dir.logFC

# Calculating directionality index with Dixon's method.
dixon.stat <- sign(up.counts-down.counts)*2*(
    (up.counts-down.counts)/(up.counts+down.counts))^2
dixon.stat

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