RVFam (version 1.1)

coxph.EC: function for testing a single/pooled variant for survival traits with family data using Cox proportional hazards regression model

Description

Fit Cox proportional hazards regression model to test a single/pooled variant for associations against a survival phenotype with family data. The coxph function from package survival is used.

Usage

coxph.EC(snp,phen,test.dat,covar,chr,time)

Arguments

snp

a numeric vector with genotype of a single/pooled variant

phen

a character string for the phenotype name of a continuous trait of interest in test.dat

test.dat

the product of merging phenotype, genotype and pedigree data

covar

a character vector for covariates in test.dat

chr

chromosome number

time

the character string of variable named for survival time

Value

ntotal

number of individuals with genotype, phenotype and covariates

nmiss

number of individuals with missing genotype among ntotal

maf_ntotal

minor allele frequency based on ntotal

beta

regression coefficient of single SNP test or burden test

se

standard error of beta

Z

Z statistic based on signed LRT

remark

additional information of the analysis

p

LRT p-value of a single variant test or burden test

MAC

minor allele count

n0

the number of individuals with 0 copy of coded alleles

n1

the number of individuals with 1 copy of coded alleles

n2

the number of individuals with 2 copies of coded alleles

Details

The coxph.EC function fits a Cox proportional hazards regression model with shared frailty (random effect) in each pedigree to test association between a survival phenotype and a single/pooled genetic variant with additive model. The trait-SNP association test is carried out by the coxph function from package survival. P-value from likelihood ratio test (LRT) is reported. This function is called in coxph.ped function to test all single/pooled variants.

References

Therneau T (2014). A Package for Survival Analysis in S. R package version 2.37-7, http://CRAN.R-project.org/package=survival.

Terry M. Therneau and Patricia M. Grambsch (2000). Modeling Survival Data: Extending the Cox Model. Springer, New York. ISBN 0-387-98784-3.

Examples

## Not run: 
# coxph.EC(snp=rsnps.dat[,"snp1"],snp1,phen="trait2",test.dat=rsnps.dat,
# covar=c("age","sex"),chr=1,time="survival_time")## End(Not run)