gi_list_topdom: gi_list_topdom

View source: R/gi_list_topdom.R

gi_list_topdomR Documentation

gi_list_topdom

Description

This function converts a gi_list instance with ICE normalized counts into TAD annotations through an implementation of TopDom v0.0.2 (https://github.com/HenrikBengtsson/TopDom) adapted as TopDom at this package. If you're using this function, please cite TopDom according to the documentation at https://github.com/HenrikBengtsson/TopDom/blob/0.0.2/docs/

Usage

gi_list_topdom(
  gi_list,
  chrs = NULL,
  file_out = FALSE,
  fpath = NULL,
  window.size = 5,
  verbose = FALSE
)

Arguments

gi_list

List of GenomicInteractions objects where each object named with chromosomes contains intrachromosomal interaction information (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.

file_out

If true, outputs TAD annotations into files with paths beginning with fpath. Defaults to FALSE

fpath

Outputs TAD annotations into files with paths beginning in fpath.

window.size

integer, number of bins to extend. Defaults to 5.

verbose

TRUE if you would like to troubleshoot TopDom.

Value

a list instance with TAD annotation reporting for each chromosome

Examples

hic_path<-system.file("extdata", "GSE63525_HMEC_combined_example.hic",
package = "HiCDCPlus")
gi_list<-hic2icenorm_gi_list(hic_path,binsize=50e3,chrs='chr22')
tads<-gi_list_topdom(gi_list)

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