Parser for data in hic format

Parses interactions in .hic format and returns an InteractionSet object.

parseHiC(paths, binSize, conditions, replicates)

Arguments

paths

A vector of paths to .hic files.

binSize

The resolution (span of each position in number of bases) to select within the .hic files.

conditions

A vector of condition names repeated along the replicates.

replicates

A vector of replicate names repeated along the conditions.

Value

An InteractionSet.

Examples

# Path to each file
paths <- c(
    "path/to/condition-1.replicate-1.hic",
    "path/to/condition-1.replicate-2.hic",
    "path/to/condition-1.replicate-3.hic",
    "path/to/condition-2.replicate-1.hic",
    "path/to/condition-2.replicate-2.hic",
    "path/to/condition-2.replicate-3.hic"
)
# Replicate and condition of each file. Can be names instead of numbers.
conditions <- c(1, 1, 1, 2, 2, 2)
replicates <- c(1, 2, 3, 1, 2, 3)
# Resolution to select
binSize <- 500000
if (FALSE) {
    # Instantiation of data set
    hic.experiment <- parseHiC(
        paths,
        conditions = conditions,
        replicates = replicates,
        binSize = binSize
    )
}