cnvrs_create {CNVgears} | R Documentation

## Compute Copy Number Variable Regions (CNVRs)

### Description

`cnvrs_create` compute CNVRs on a `CNVResutls` object, typically the output of `inter_res_merge`.

### Usage

    cnvrs_create(cnvs, chr_arms, prop = 0.3)

### Arguments

`cnvs` | a `CNVresults` produced by `read_results`.
`chr_arms` | a `data.table` containing chromosomal arms locations. They are bundled in the package for hg18, hg19 and hg38 (`hgXX_chr_arms`).
`prop` | reciprocal overlap proportion, default 0.3 (30%).

### Details

Copy Number Variable Regions (CNVRs) are defined as groups of reciprocal overlapping CNVs. This function first try to assign every call to a CNVR (or create a new one if it is not possible), then check if adjacent CNVRs cam be merged, and finally recheck all the CNVs in each CNVRs and un-assign them if the reciprocal overlap is no longer fulfilled with all the member of the CNVR. If any event is touched by this last step, a new cycle begins, this until no more CNVs can be removed from the assigned CNVR.

### Value

a `list` of two elements. The first element is a `data.table` that contains the actual CNVR information, genomic location and frequency in the cohort. The second element is the `CNVresults`

### Examples

    DT <- cnvrs_create(penn_22, hg19_chr_arms)

[Package CNVgears version 1.0.0 Index]