combine_twogeno: Function to combine two sets of ped pairs for two samples

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

Description

Function to combine two sets of ped pairs for two samples

Usage

combine_twogeno(file1, file2, keep1 = NA, keep2 = NA, missing_cut = 0.5)

Arguments

file1	the file name for the first sample before the extension. Eg. file1=sample1 if the file names are sample1.ped/map
file2	the file name for the second sample before the extension. Eg. file1=sample2 if the file names are sample2.ped/map
keep1	if only a subset of sample1 is needed in the final analyis, keep1=1, ow, keep1=NA
keep2	if only a subset of sample2 is needed in the final analyis, keep2=1, ow, keep2=NA
missing_cut	the missing rate to remove the high-missing variants

Value

a list include data sets 'common' and 'rare' for common or rare variants and 'snp.Nomiss' for the SNPs kept in common and rare.

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