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

Description Usage Arguments Value

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

1
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.