treediff (version 0.2.2)

HiC2Tree: Convert Hi-C to trees

Description

This function converts Hi-C data into trees, using adjClust. It takes as input a file path vector, the format of the input data, the bin size of the Hi-C array, the chromosomes to be included in the analysis, and the number of replicates. It returns a list containing all trees, metadata, index and treediff results.

Usage

HiC2Tree(files, format, binsize = NULL, index = NULL, chromosomes, replicates)

Value

A list containing:

trees

A list of all trees.

metadata

A data frame containing the following columns: names (name of each tree), chromosome, cluster, and file.

index

A data table containing the correspondence of each bin in the genome.

testRes

A list of treediff results for each cluster.

Arguments

files

A character vector containing the file paths of the input data.

format

A character vector indicating the format of the input data: "tabular", "cooler", "juicer", or "HiC-Pro".

binsize

An integer indicating the bin size of the Hi-C matrix.

index

A character indicating the path of the index for the input data. Required (and used) only with the "HiC-Pro" format.

chromosomes

A vector containing the chromosomes to be included in the analysis.

replicates

An integer indicating the number of replicates to be used in treediff.

References

Christophe Ambroise, Alia Dehman, Pierre Neuvial, Guillem Rigaill, and Nathalie Vialaneix (2019) Adjacency-constrained hierarchical clustering of a band similarity matrix with application to genomics. Algorithms for Molecular Biology, 14(22), 363–389.

Examples

replicates <- 1:3
cond <- c("90", "110")
all_begins <- interaction(expand.grid(replicates, cond), sep = "-")
all_begins <- as.character(all_begins)

# single chromosome
nb_chr <- 1
chromosomes <- 1:nb_chr
all_mat_chr <- lapply(chromosomes, function(chr) {
  all_mat <- lapply(all_begins, function(ab) {
    mat_file <- paste0("Rep", ab, "-chr", chr, "_200000.bed")
  })
  all_mat <- unlist(all_mat)
})
index <- system.file("extdata", "index.200000.longest18chr.abs.bed",
                     package = "treediff")
format <- rep("HiC-Pro", length(replicates) * length(cond) * nb_chr)
binsize <- 200000
files <- system.file("extdata", unlist(all_mat_chr), package = "treediff")
replicates <- c(3, 3)
HiC2Tree(files, format, binsize, index, chromosomes, replicates)

if (FALSE) {
# two chromosomes
nb_chr <- 2
chromosomes <- 1:nb_chr
all_mat_chr <- lapply(chromosomes, function(chr) {
  all_mat <- lapply(all_begins, function(ab) {
    mat_file <- paste0("Rep", ab, "-chr", chr, "_200000.bed")
  })
  all_mat <- unlist(all_mat)
})
files <- system.file("extdata", unlist(all_mat_chr), package = "treediff")
format <- rep("HiC-Pro", length(replicates) * length(cond) * nb_chr)
replicates <- c(3, 3)
HiC2Tree(files, format, binsize, index, chromosomes, replicates)
}