vcf_process: the main function to call the VCF file and return the...

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

Description

the main function to call the VCF file and return the expected probabilities of the genotypes E(G_ij|D_ij) from VCF file

Usage

  vcf_process(file = "example/1g113low_1g56exomehigh_filtered.hg19.chr11_1000snps.vcf",
  caseID_file = "example/caseID.txt", nhead = 128, ncol_ID = 9,
  missing_th = 0.2, nvar_tot = 1000, nread = 300, maf_cut = 0.05,
  common = TRUE)

Arguments

file	the VCF file
caseID_file	the caseID files
nhead	the row number of your VCF which contains all sample ID
ncol_ID	the number of columns before the sample ID
missing_th	the missing rate cut off for a SNP to be filtered, if missing>missing_th in case or controls, the SNP will be removed
nvar_tot	should be the number of SNPs in your VCF file, but if VCF is too large, you can choose only read in the first nsnp SNPs
nread	the number of SNPs read each time by R (nread<=nsnp)
maf_cut	the MAF to be used to filter out SNP,
common	Boolean variable to indicate common (TRUE) or rare (FALSE) variants

Value

a list for case or control (depends on group) including expected conditional probabilities, SNP info, Y, ncase/ncont etc

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