Parser for data in cool format

Parses interactions in .cool or .mcool format and returns an InteractionSet object.

parseCool(paths, binSize = NA, conditions, replicates)

Arguments

paths

A vector of paths to .cool or .mcool files.

binSize

The resolution (span of each position in number of bases). Optionally provided to select the appropriate resolution in .mcool files. Defaults to NULL.

conditions

A vector of condition names repeated along the replicates.

replicates

A vector of replicate names repeated along the conditions.

Value

An InteractionSet.

Details

To read .cool of .mcool files, the rhdf5 package is required. Please install it before running the function.

Examples

# EXAMPLE FOR .cool FORMAT
# Path to each file
pathsCool <- c(
    "path/to/condition-1.replicate-1.cool",
    "path/to/condition-1.replicate-2.cool",
    "path/to/condition-1.replicate-3.cool",
    "path/to/condition-2.replicate-1.cool",
    "path/to/condition-2.replicate-2.cool",
    "path/to/condition-2.replicate-3.cool"
)
# Condition and replicate 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)
if (FALSE) {
    library(rhdf5)
    object <- parseCool(
        paths,
        conditions = conditions,
        replicates = replicates
    )
}

# EXAMPLE FOR .mcool FORMAT
# Resolution
binSize <- 500000
# Path to each file
paths <- c(
    "path/to/condition-1.replicate-1.mcool",
    "path/to/condition-1.replicate-2.mcool",
    "path/to/condition-1.replicate-3.mcool",
    "path/to/condition-2.replicate-1.mcool",
    "path/to/condition-2.replicate-2.mcool",
    "path/to/condition-2.replicate-3.mcool"
)
# Condition and replicate 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)
if (FALSE) {
    # Instantiation of data set
    library(rhdf5)
    object <- parseCool(
        paths,
        conditions = conditions,
        replicates = replicates,
        binSize = binSize
    )
}