statusFromTriostate: Extract inheritance status from penn trio string collapsing...

In aksenia/SeeCiTe: Assess the quality of and visualize array CNV callset for trios

Description

Extract inheritance status from penn trio string collapsing copy number strings to discrete "del", "dup", "normal" or ""copy-neutrLOH" following PennCNV encoding (Wang et al, 2007)

Usage

statusFromTriostate(penntriostate, offspring_order = 1)

Arguments

penntriostate	A string of three digits representing copynumber state for members of a trio/quad
offspring_order	Can be used both on trios and quads, therefore the index of an offspring (1 or 2) needs to be specified. Defaut is 1. (a trio)

Value

A string with a status, one of "denovo"/"inherited"

Examples

statusFromTriostate("323")

aksenia/SeeCiTe documentation built on Jan. 19, 2021, 12:35 a.m.