add_hic_counts: add_hic_counts

In mervesa/HiCDCPlus: Hi-C Direct Caller Plus

add_hic_counts

Description

This function adds counts from a .hic file into a valid, binned, gi_list instance.

Usage

add_hic_counts(gi_list, hic_path, chrs = NULL, add_inter = FALSE)

Arguments

gi_list	valid, uniformly binned gi_list instance. See ?gi_list_validate and gi_list_binsize_detect for details.
hic_path	path to the .hic file
chrs	a subset of chromosomes' e.g., c('chr21','chr22'). Defaults to all chromosomes in the gi_list instance.
add_inter	Interchromosomal interaction counts added as a 1D feature named 'inter' on regions metadata handle of each gi_list element (e.g., gi_list[[1]]@regions@elementMetadata or not; default FALSE

Value

gi_list instance with counts on the metadata (e.g., mcols(gi_list[[1]]) handle on each list element, and 'inter' on regions metadata handle of each element if add_inter=TRUE.

Examples

gi_list<-generate_binned_gi_list(50e3,chrs='chr22')
gi_list<-add_hic_counts(gi_list,
hic_path=system.file("extdata", "GSE63525_HMEC_combined_example.hic",
package = "HiCDCPlus"))

mervesa/HiCDCPlus documentation built on June 8, 2022, 3:43 a.m.