# An R package for analysis of case-control studies in genetic epidemiology

## Documentation for package ‘CGEN’ version 3.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

additive.test | A test for gene-environment interaction under an additive risk model for case-control data
CGEN | An R package for analysis of case-control studies in genetic epidemiology
chromosome.plot | Chromosome plot
getMatchedSets | Case-Control and Nearest-Neighbor Matching
getSummary | Compute summary information
getWaldTest | Compute a Wald test
GxE.scan | GxE analysis for an array of SNPs
GxE.scan.combine | Combines output files into one file
GxE.scan.partition | Creates GxE.scan job files for a computing cluster
locusMap.list | List to describe the locus map data
LocusMapData | Locus map data
pheno.list | List to describe the covariate and outcome data
printEffects | Print an effects table
QQ.plot | QQ plot
recode.geno | Recode a vector of genotypes
sas.list | List for SAS data sets
score.test | A test for gene-environment interaction under an additive risk model for case-control data
snp.effects | Joint and Stratified Effects
snp.effects.plot | Effects plot
snp.list | List to describe the genotype data
snp.logistic | Logistic regression analysis for a single SNP
snp.matched | Robust G-G and G-E Interaction with Finely-Matched Case-Control Data.
snp.scan.logistic | Logistic regression analysis for an array of SNPs
SNPdata | Sample genotype data
subject.list | List to describe the file of subject ids
Xdata | Sample covariate and outcome data