HTClist2gi_list: HTClist2gi_list

In mervesa/HiCDCPlus: Hi-C Direct Caller Plus

HTClist2gi_list

Description

This function converts a HTClist instance into a gi_list instance with counts for further use with this package, HiCDCPlus

Usage

HTClist2gi_list(htc_list, chrs = NULL, Dthreshold = 2e+06)

Arguments

htc_list	A valid HTClist instance (see vignette("HiTC"))
chrs	select a subset of chromosomes' e.g., c('chr21','chr22'). Defaults to chromosomes in htc_list.
Dthreshold	maximum distance (included) to check for significant interactions, defaults to 2e6 or maximum in the data; whichever is smaller.

Value

a thresholded gi_list instance with intra-chromosomal counts for further use with HiCDCPlus

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)
gi_list2<-HTClist2gi_list(htc_list,Dthreshold=Inf)

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