aSPU (version 1.36)

getlogitp: Get the p-values of the multiple SNPs based on the Wald test in a logistic regresion model.

Description

Get p-value using logistic regresion for each of the multiple SNPs

Usage

getlogitp(Y, X)

Arguments

Y

Response or phenotype data. It can be a disease indicator; =0 for controls, =1 for cases.

X

Genotype or other data; each row for a subject, and each column for an SNP (or a predictor). The value of each SNP is the # of the copies for an allele. A matrix with dimension n by p (n : number of observation, p : number of SNPs (or predictors)

Value

• p-values for each SNPs.

See Also

GATES2 GatesSimes Hyst

Examples

simula <- simPathAR1Snp(nGenes=20, nGenes1=1, nSNPlim=c(1, 20), nSNP0=1:3,
                           LOR=.2, rholim=c(0,0),
                           n=100, MAFlim=c(0.05, 0.4), p0=0.05)
logitp <- getlogitp(simula$Y, simula$X)