construct_features_chr {HiCDCPlus} | R Documentation

## construct_features_chr

### Description

This function lists all restriction enzyme cutsites of a given genome and genome version with genomic features outlined in Carty et al. (2017) for a single chromosome. https://www.nature.com/articles/ncomms15454; GC content, mappability, and effective length

### Usage

    construct_features_chr(
      chrom,
      gen = "Hsapiens",
      gen_ver = "hg19",
      sig = "GATC",
      bin_type = "Bins-uniform",
      binsize = 5000,
      wg_file = NULL,
      feature_type = "RE-based"
    )

### Arguments

`chrom` | select a chromosome.
`gen` | name of the species: e.g., default `'Hsapiens'`.
`gen_ver` | genomic assembly version: e.g., default `'hg19'`.
`sig` | restriction enzyme cut pattern (or a vector of patterns; e.g., 'GATC' or c('GATC','GANTC')).
`bin_type` | 'Bins-uniform' if uniformly binned by binsize in bp, or 'Bins-RE-sites' if binned by number of restriction enzyme fragments.
`binsize` | binsize in bp if bin_type='Bins-uniform' (or number of RE fragment cut sites if bin_type='Bins-RE-sites'), defaults to 5000.
`wg_file` | path to the bigWig file containing mappability values across the genome of interest.
`feature_type` | 'RE-based' if features are to be computed based on restriction enzyme fragments. 'RE-agnostic' ignores restriction enzyme cutsite information and computes features gc and map based on binwide averages. bin_type has to be 'Bins-uniform' if `feature_type='RE-agnostic'`.

### Value

a features 'bintolen' file that contains GC, mappability and length features.

### Examples

    df<-construct_features_chr(chrom='chr22',
    gen='Hsapiens', gen_ver='hg19',sig=c('GATC','GANTC'),bin_type='Bins-uniform',
    binsize=100000,wg_file=NULL)

[Package HiCDCPlus version 1.0.0 Index]