add_hicpro_matrix_counts: add_hicpro_matrix.counts

In mervesa/HiCDCPlus: Hi-C Direct Caller Plus

add_hicpro_matrix.counts

Description

This function converts HiC-Pro matrix and bed outputs into a gi_list instance.

Usage

add_hicpro_matrix_counts(
  gi_list,
  absfile_path,
  matrixfile_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.
absfile_path	absfile BED out of HiC-Pro (e.g., 'rawdata_10000_abs.bed')
matrixfile_path	matrix count file out of HiC-Pro (e.g., 'rawdata_10000.matrix')
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.

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