cc.sim: case control simulation

In HAP.ROR: Recursive Organizer (ROR)

Description

simulating case-control data given causal amino acids/haplotype alleles

Usage

cc.sim(n.ctrl, n.case, beta0, beta1, case.sub, ctl.sub, lib.sub, lib.sub.names, risk.type = "AA", risk.inx = 2, risk.names = c("301", "302"), min.count = 10, ctl.only = FALSE)

Arguments

n.ctrl	number of control samples desired to generate
n.case	number of case samples desired to generate
beta0	the coefficient of intercept for logistic model
beta1	the coefficient of the causal SNP for logistic model
case.sub	case subjects, two columns for two haplotypes
ctl.sub	control subjects, two columns for two haplotypes
lib.sub	the alleles library contains allele sequences for those only appear in the case and control samples
lib.sub.names	the corresponding names of the alleles
risk.type	risk.type="AA": simulated from given amino acid position as shown in matrix lib.sub, use risk.inx to input position risk.type="allele":simulated from given risk alleles, use risk.names=c("301", "302") to specified those alleles
risk.inx	the given amino acid position
risk.names	allele names
min.count	use to calculate the warning if the selected alleles have too small frequencies
ctl.only	use control only to simulate or not

Value

y	phenotype
x	simulated samples
risk.names	the input risk allele names
select.freq	simulated allele frequencies

Author(s)

Xin Huang

HAP.ROR documentation built on May 1, 2019, 10:24 p.m.