get_IDs: Function to seprates the case and control IDs.

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 read the header of the vcf file (rows starting with # in vcf) and split the case and controls according to the caseID_file. It returns two vectors each of which is the position index of case or control in the list of samples in vcf file (the last row starting with #).

Usage

get_IDs(vcf_file, caseID_file, nhead = 128, ncol_ID = 9)

Arguments

vcf_file	The saving address and filename of the vcf file in the format of 'address/filename'.
caseID_file	The file including case IDs in the format of 'address/filename'.
nhead	The number of the lines in the vcf file which started with #.
ncol_ID	The number of columns before the sample IDs start in the last line of the headers in the vcf file, default=9.

Value

a list which inclues two vectors that correspond to the position index of the cases or controls in the last head row of the VCF with IDs, but columns are shifted by the ncol_ID columns.

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