gi_list_topdom: gi_list_topdom

In mervesa/HiCDCPlus: Hi-C Direct Caller Plus

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.