HTClist2gi_list {HiCDCPlus} | R Documentation

## 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)

[Package HiCDCPlus version 1.0.0 Index]