extract_hic_eigenvectors {HiCDCPlus} | R Documentation

## extract_hic_eigenvectors

### Description

This function uses Juicer command line tools to extract first eigenvectors across chromosomes from counts data in a .hic file and outputs them to text file of the structure chr start end score where the score column contains the eigenvector elements.

### Usage

    extract_hic_eigenvectors(
      hicfile,
      mode = "KR",
      binsize = 1e+05,
      chrs = NULL,
      gen = "Hsapiens",
      gen_ver = "hg19"
    )

### Arguments

`hicfile` | path to the input .hic file.
`mode` | Normalization mode to extract first eigenvectors from Allowable options are: 'NONE' for raw (normalized counts if .hic file is written using `hicdc2hic` or `hic2icenorm_gi_list`), 'KR' for Knight-Ruiz normalization, 'VC' for Vanilla-Coverage normalization and 'VC_SQRT' for square root vanilla coverage. Defaults to 'KR'.
`binsize` | the uniform binning size for compartment scores in bp. Defaults to 100e3.
`chrs` | a subset of chromosomes' e.g., c('chr21','chr22'). Defaults to all chromosomes except "Y", and "M" for the specified `gen` and `gen_ver`.
`gen` | name of the species: e.g., default `'Hsapiens'`.
`gen_ver` | genomic assembly version: e.g., default `'hg19'`.

### Value

path to the eigenvector text files for each chromosome containing chromosome, start, end and compartment score values that may need to be flipped signs for each chromosome. File paths follow `gsub('.hic','_<chromosome>_eigenvectors.txt',hicfile)`

### Examples

    eigenvector_filepaths<-extract_hic_eigenvectors(
    hicfile=system.file("extdata", "GSE63525_HMEC_combined_example.hic",
    package = "HiCDCPlus"),
    chrs=c("chr22"),binsize=50e3)

[Package HiCDCPlus version 1.0.0 Index]