cnvrs_create: Compute Copy Number Variable Regions (CNVRs)

In SinomeM/CNVgears: A Framework to Combine, Analize and Interpret CNVs Calling Results

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)

SinomeM/CNVgears documentation built on Nov. 21, 2021, 5:34 a.m.