generate_bintolen_gi_list {HiCDCPlus} | R Documentation

## 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)

[Package HiCDCPlus version 1.0.0 Index]