Constructs a HiCDOCDataSet from a set of HiC-Pro generated files.

HiCDOCDataSetFromHiCPro(matrixPaths, bedPaths, replicates, conditions)

Arguments

matrixPaths

A vector of paths to HiC-Pro matrix files.

bedPaths

A vector of paths to HiC-Pro bed files.

replicates

A vector of replicate names repeated along the conditions.

conditions

A vector of condition names repeated along the replicates.

Value

A HiCDOCDataSet.

Examples

if (FALSE) { # Path to each matrix file matrixPaths = c( 'path/to/condition-1.replicate-1.matrix', 'path/to/condition-1.replicate-2.matrix', 'path/to/condition-2.replicate-1.matrix', 'path/to/condition-2.replicate-2.matrix', 'path/to/condition-3.replicate-1.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-2.replicate-1.bed', 'path/to/condition-2.replicate-2.bed', 'path/to/condition-3.replicate-1.bed' ) # Replicate and condition of each file. Can be names instead of numbers. replicates <- c(1, 2, 1, 2, 1) conditions <- c(1, 1, 2, 2, 3) # Instantiation of data set hic.experiment <- HiCDOCDataSetFromHiCPro( matrixPaths = matrixPaths, bedPaths = bedPaths, replicates = replicates, conditions = conditions ) }