generate_seqdata_OR: Function to simulate data for one variant by given parameters

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 simulate data for one variant by given parameters

Usage

generate_seqdata_OR(N, preval, ncase, ncont, mafco, OR, mdcase, sdcase, mdcont,
  sdcont, me, sde, nsnp)

Arguments

N	population size
preval	prevalence rate for the disease
ncase	the number of case
ncont	the number of controls
mafco	MAF for controls
OR	the odds ratio
mdcase	average read depth in cases (double) >0#' @param sddcase, standard deviation of read depth in cases (double) >0
mdcont	average read depth in controls (double) >0
sde	standard deviation of error rate (double) >0
nsnp	number of variant
Ncont	number of controls
sddcont	standard deviation of read depth in controls (double) >0#' @param me, average error rate, probability that sequence call is wrong (double) >0

Value

MM - conditional expected value E(Gij|Dij)

P -estimated genotype frequencies P(G=0), P(G=1), P(G=2)

G - true genotype from which sequence data generated

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