cnvrs_create: Compute Copy Number Variable Regions (CNVRs)

In SinomeM/QCtreeCNV: Reducing the visual inspection effort in CNV calling

Compute Copy Number Variable Regions (CNVRs)

Description

cnvrs_create compute CNVRs from a list of CNVs.

Usage

cnvrs_create(cnvs, chr_arms, prop = 0.3, final_merge = T)

Arguments

cnvs	lorem ipsum
chr_arms	lorem ipsum
prop	reciprocal overlap proportion, default 0.3 (30%).
final_merge	lorem ipsum

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

SinomeM/QCtreeCNV documentation built on Dec. 5, 2023, 4:06 p.m.