loadData: Load and Normalize Hi-C Data

In hicream: HI-C diffeREntial Analysis Method

Load and Normalize Hi-C Data

Description

This function loads data necessary for the analysis and outputs them in a suitable format for performTest and 2Dclust.

Usage

loadData(files, index, chromosome, normalize = TRUE)

Arguments

files	character vector. Paths to Hi-C matrices in bed format.
index	character. A path to an index file in bed format.
chromosome	character or integer. Chromosome to select.
normalize	logical. Whether or not to normalize the output (with MA method). Set to TRUE by default.

Value

An InteractionSet corresponding to all interactions present in at least one of the input matrices and corresponding counts across all matrices.

Author(s)

Élise Jorge [e-mail]
Sylvain Foissac [e-mail]
Pierre Neuvial [e-mail]
Nathalie Vialaneix [e-mail]

Examples

replicates <- 1:2
cond <- "90"
allBegins <- interaction(expand.grid(replicates, cond), sep = "-")
allBegins <- as.character(allBegins)
chromosome <- 1
nbChr <- 1
allMat <- sapply(allBegins, function(ab) {
  matFile <- paste0("Rep", ab, "-chr", chromosome, "_200000.bed")
  })
index <- system.file("extdata", "index.200000.longest18chr.abs.bed",
                    package = "hicream")
                    format <- rep("HiC-Pro", length(replicates) * length(cond) * nbChr)
binsize <- 200000
files <- system.file("extdata", unlist(allMat), package = "hicream")
exData <- loadData(files, index, chromosome, normalize = TRUE)

hicream documentation built on Aug. 8, 2025, 7:26 p.m.