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


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Documentation for package ‘CGEN’ version 3.12.1

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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
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
Manhattan.plot Manhattan plot
pheno.list List to describe the covariate and outcome data
printEffects Print an effects table
QQ.plot QQ plot
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.score Score Test
subject.list List to describe the file of subject ids
Xdata Sample covariate and outcome data