get_CNV: Function to get the locations of copy number variations

In HiCcompare: HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets

Description

Function to get the locations of copy number variations

Usage

get_CNV(path2bam, out.file = "CNV_calls", bin.size = 1000,
  genome = "hg19", CNV.level = 2)

Arguments

path2bam	The path to the folder containing the .bam files for the data
out.file	The prefix for the filename which will be exported.
bin.size	The bin.size (resolution) of the HiC data you will be using in kbp. e.g. for 1MB resolution enter 1000, for 500kb resolution enter 500. The available bin sizes for hg19 1, 5, 10, 15, 30, 50, 100, 500, and 1000 kbp
genome	Character string for the genome. Defaults to 'hg19'.
CNV.level	The value require to call a region a CNV. Should be either 1, or 2. This setting will determine what level of CNV will be returned in the resulting BED file. 1 indicates any copy number variation will be returned. 2 indicates only deletions and amplifications will be returned. Defaults to 2.

Details

This function utilizeds QDNAseq to detect CNV (copy number variations) in your Hi-C data. You must have the .bam files in order to use this function. Place the .bam files in a folder and set path2bam as the path to this folder. The function will then perform CNV detection and export a .txt file containing the CNV calls for each region of the genome. In addition the results will be returned from the function as a data.frame. It is reccomended to exclude the regions with extreme CNV when using HiCcompare. Regions can be excluded using the create.hic.table() function. For more information about the methods used in this function see QDNAseq here: https://bioconductor.org/packages/release/bioc/html/QDNAseq.html

Value

A data.frame containing the regions for CNVs at the level specified with the CNV.level option. A data.frame containing the calls for all regions will also be written to the disk using the out.file prefix. The first 4 columns of the data.frame contain location information for the genomic regions. All following columns contain the CNV calls for each .bam file. CNV calls are defined as follows: -2 = deletion, -1 = loss, 0 = normal, 1 = gain, 2 = amplification. Additionally, a .bed file will be written to disk containing the same values as the returned data.frame.

Examples

## Not run: 
cnv_calls <- get_CNV(path2bam = 'C:/bamfiles')

## End(Not run)

HiCcompare documentation built on Nov. 8, 2020, 8:26 p.m.