nRec: Variant filtering with recessive inheritance

In BartBroeckx/Mendelian: Variant Analysis for Mendelian Disorders

Description

nRec should be used to filter variants under a recessive mode of inheritance.

Usage

nRec(x, y, family)

Arguments

x	the case(s).
y	optional, the control(s).
family	optional, "P-F" or "Ps-F" mode, indicating a (healthy) parent(s)- (affected) progeny relation.

Details

nRec checks for common variants that are homozygous in the cases. If variants from control(s) are present, they can be used to filter variants from the cases. However, only homozygous variants are used to filter. In addition, various detectance and penetrance parameters can be specified during the processing.

If family is specified, penetrance is assumed to be complete. In addition, the causal variant is assumed to be homozygous in the case and heterozygous in the parent(s).

Author(s)

Bart Broeckx

Examples

output <- nRec("CLCfile1", "CLCfile2")
output
output <- nRec(c("CLCfile1","CLCfile2"))
output

BartBroeckx/Mendelian documentation built on May 5, 2019, 10:27 a.m.