coxph.EC: function for testing a single/pooled variant for survival...

In RVFam: Rare Variants Association Analyses with Family Data

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

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.

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

Author(s)

Ming-Huei Chen <[e-mail]> and Qiong Yang <[e-mail]>

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)

RVFam documentation built on May 2, 2019, 8:26 a.m.