get_exp_MAF: Function to calculate the minor allele frequency (MAF) from...

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

Description

It calculates the MAF from conditional expected genotype probability and returns the matrices of expected genotype probability and genotype frequncy for variants indicated by maf_cut and group which are to be inputed into a test function of the rvs package.

Usage

get_exp_MAF(P, MM, chr, loc, ncase, maf_cut = 0.05, common = common)

Arguments

P	genotype frequency for the whole sample which is the output of function get_exp_geno.
MM	expected genotype probability, output of function get_exp_geno.
chr	the chrom info of each variant
loc	the location info of each variant
ncase	integer, the number of cases
maf_cut	the minor allele frequency cut-off for common or rare variants
common	Boolean variable to indicate common or rare variants

Value

matrix of genotype frequency (P), expected genotype probability (Geno) and variant information (SNPs), number of case (ncase), number of control (ncont) and number of variants (nsnp) and a vector for phenotyp (Y).

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