generate_bintolen_gi_list: generate_bintolen_gi_list

In mervesa/HiCDCPlus: Hi-C Direct Caller Plus

generate_bintolen_gi_list

Description

Generates a gi_list instance from a bintolen file generated by generate.features (see ?generate.features) for details).

Usage

generate_bintolen_gi_list(
  bintolen_path,
  chrs = NULL,
  Dthreshold = 2e+06,
  binned = TRUE,
  binsize = NULL,
  gen = "Hsapiens",
  gen_ver = "hg19"
)

Arguments

bintolen_path	path to the flat file containing columns named bins and features
chrs	select a subset of chromosomes' e.g., c('chr21','chr22'). Defaults to all chromosomes specified in the bintolen file.
Dthreshold	maximum distance (included) to check for significant interactions, defaults to 2e6 or maximum in the data; whichever is smaller.
binned	TRUE if the bintolen file is uniformly binned. Defaults to TRUE.
binsize	bin size in bp to be generated for the object. Defaults to the binsize in the bintolen file, if exists.
gen	name of the species: e.g., default 'Hsapiens'
gen_ver	genomic assembly version: e.g., default 'hg19'

Value

a valid gi_list instance with genomic features derived from specified restriction enzyme cut patterns when generating the bintolen file using construct_features (see ?construct_features for help). Genomic 1D features are stored in the regions metadata handle of each list element (e.g., gi_list[[1]]@regions@elementMetadata).

Examples

chrs<-'chr22'
bintolen_path<-system.file("extdata", "test_bintolen.txt.gz",
package = "HiCDCPlus")
gi_list<-generate_bintolen_gi_list(bintolen_path,chrs)

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