gi_list2HTClist: gi_list2HTClist

In mervesa/HiCDCPlus: Hi-C Direct Caller Plus

gi_list2HTClist

Description

This function converts a gi_list instance into a HTClist instance compatible for use with the R Bioconductor package HiTC https://bioconductor.org/packages/HiTC/

Usage

gi_list2HTClist(gi_list, chrs = NULL)

Arguments

gi_list	List of GenomicInteractions objects with a counts column where each object named with chromosomes contains intra-chromosomal interaction information (minimally containing counts and genomic distance in mcols(gi_list)— see ?gi_list_validate for a detailed explanation of valid gi_list instances).
chrs	select a subset of chromosomes' e.g., c('chr21','chr22'). Defaults to chromosomes in gi_list.

Value

a HTClist instance compatible for use with HiTC

Examples

gi_list<-generate_binned_gi_list(50e3,chrs=c('chr22'))
gi_list<-add_hic_counts(gi_list,
hic_path<-system.file("extdata", "GSE63525_HMEC_combined_example.hic",
package = "HiCDCPlus"))
htc_list<-gi_list2HTClist(gi_list)

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