Estimate Gene-Treatment Interaction Exploiting Randomization

Documentation for package ‘TwoPhaseInd’ version 1.1.2

aco1arm	A function to estimate parameters in augmented case-only designs, the genotype is ascertained for a random subcohort from the active treatment arm or the placebo arm.
aco2arm	A function to estimate parameters in Cox proportional hazards model using augmented case-only designs, the genotype is ascertained for a random subcohort from both the active treatment arm and the placebo arm (case-cohort sampling) or a case-control sample in both arms.
acoarm	A function to estimate parameters in Cox proportional hazard models by augmented case-only designs for randomized clinical trials with failure time endpoints.
acodata	A dataset from the STEP trial to study the interactions between gene and vaccine on HIV infection
caseonly	A function to deal with case-only designs
char2num	A function used in acoarm to transform categorical variable to integers
mele	function to compute the maximum estimated likelihood estimator
remove_missingdata	A function used in acoarm to remove missing data
remove_rarevariants	A function used in spmle and acoarm to remove rare-variant covariates
spmle	function to compute the semiparametric maximum likelihood estimator
whiBioMarker	An example dataset to demostrate the usage of MELE and SPMLE