ped_2_additive: Function to combine two ped files for case and controls and...

In Struglab/RVS: Robust Variance Score (RVS) test for association of variants from next generation sequence data with binary traits using external controls

Description

This function remove variants that are missing in one sample, monomorphic in whole sample, monomorphic in each sample with diff alleles, non biallelic Alternatively, for those know plink, all these can be done by plink to merge the two files and generate the additive coding with option –recodeA

Usage

ped_2_additive(M1, M2, ncols)

Arguments

M1	the genotype data for the first sample (normally case)
M2	the genotype data for the secondsample (normally controls)
ncols	the number of column before the genotype data start

Value

A list including - Ad_all: the additive coding for all snps left, ncase: the first ncase rows are for cases; minor: the minor allele for each variants; rmed, the index of the removed snps from the input

Struglab/RVS documentation built on May 9, 2019, 3:11 p.m.