domainDirections: Calculate domain directionality
In diffHic: Differential Analyis of Hi-C Data

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

Collect directionality statistics for domain identification with genomic bins.

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

`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

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.

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.

Aaron Lun

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

squareCounts

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