add_hicpro_allvalidpairs_counts: add_hicpro_allvalidpairs_counts

In mervesa/HiCDCPlus: Hi-C Direct Caller Plus

add_hicpro_allvalidpairs_counts

Description

This function converts HiC-Pro outputs in allValidPairs format into a gi_list instance.

Usage

add_hicpro_allvalidpairs_counts(
  gi_list,
  allvalidpairs_path,
  chrs = NULL,
  binned = TRUE,
  add_inter = FALSE
)

Arguments

gi_list	valid gi_list instance. See ?gi_list_validate for details. You can also detect whether a gi_list instance is uniformly binned, along with its bin size using gi_list_binsize_detect.
allvalidpairs_path	allValidPairsfile obtained from HiC-Pro (e.g., 'GSM2572593_con_rep1.allvalidPairs.txt')
chrs	a subset of chromosomes' e.g., c('chr21','chr22'). Defaults to all chromosomes in the gi_list instance.
binned	TRUE if the gi_list instance is uniformly binned (helps faster execution). Defaults to TRUE.
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.