Parser for HiCPro data

Parses interactions in pairs of .matrix and .bed files and returns an InteractionSet object.

parseHiCPro(matrixPaths, bedPaths, conditions, replicates)

Arguments

matrixPaths

A vector of paths to HiC-Pro matrix files.

bedPaths

A vector of paths to HiC-Pro bed 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 matrix file
matrixPaths <- c(
    "path/to/condition-1.replicate-1.matrix",
    "path/to/condition-1.replicate-2.matrix",
    "path/to/condition-1.replicate-3.matrix",
    "path/to/condition-2.replicate-1.matrix",
    "path/to/condition-2.replicate-2.matrix",
    "path/to/condition-2.replicate-3.matrix"
)

# Path to each bed file
bedPaths <- c(
    "path/to/condition-1.replicate-1.bed",
    "path/to/condition-1.replicate-2.bed",
    "path/to/condition-1.replicate-3.bed",
    "path/to/condition-2.replicate-1.bed",
    "path/to/condition-2.replicate-2.bed",
    "path/to/condition-2.replicate-3.bed"
)

# 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
    hic.experiment <- parseHiCPro(
        matrixPaths = matrixPaths,
        bedPaths = bedPaths,
        conditions = conditions,
        replicates = replicates
    )
}