gi_list_read: gi_list_read

In mervesa/HiCDCPlus: Hi-C Direct Caller Plus

gi_list_read

Description

Reads a written gi_list instance using gi_list_write into a valid gi_list instance.

Usage

gi_list_read(
  fname,
  chrs = NULL,
  Dthreshold = NULL,
  features = NULL,
  gen = "Hsapiens",
  gen_ver = "hg19"
)

Arguments

fname	path to the file to read from (can end with .txt, .rds, or .txt.gz).
chrs	select a subset of chromosomes' e.g., c('chr21','chr22'). Defaults to all chromosomes contained in the fname.
Dthreshold	maximum distance (included) to check for significant interactions, defaults to the maximum in the data.
features	Select the subset of features (1-D or 2-D) to be added to the gi_list instance (without the trailing I or J), defaults to all features (score column gets ingested as 'score').
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 1D features stored in regions metadata handle of each list element (e.g., gi_list[[1]]@regions@elementMetadata) in the instance and with 2D features stored in metadata handle (i.e., mcols(gi)).

Examples

outputdir<-paste0(tempdir(check=TRUE),'/')
gi_list<-generate_binned_gi_list(1e6,chrs='chr22')
gi_list_write(gi_list,paste0(outputdir,'testgiread.txt'))
gi_list2<-gi_list_read(paste0(outputdir,'testgiread.txt'))

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