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

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

AuthorSamsiddhi Bhattacharjee, Nilanjan Chatterjee, Summer Han and William Wheeler
Date of publicationNone
MaintainerWilliam Wheeler <wheelerb@imsweb.com>
LicenseGPL-2 + file LICENSE
Version3.10.0

View on Bioconductor

Functions

additive.test Man page
CGEN Man page
getMatchedSets Man page
getSummary Man page
getWaldTest Man page
GxE.scan Man page
GxE.scan.combine Man page
GxE.scan.partition Man page
LocusMapData Man page
locusMap.list Man page
Manhattan.plot Man page
pheno.list Man page
printEffects Man page
QQ.plot Man page
snp.effects Man page
snp.effects.plot Man page
snp.list Man page
snp.logistic Man page
snp.matched Man page
snp.score Man page
subject.list Man page
Xdata Man page

Files

CGEN/DESCRIPTION
CGEN/LICENSE
CGEN/NAMESPACE
CGEN/NEWS
CGEN/R
CGEN/R/Modified_Wald_Test_Sandwich_v3.R
CGEN/R/R_Pdg.xs.strat.dom.r
CGEN/R/R_RERI.AP.S.r
CGEN/R/R_RERI.AP.S.small.r
CGEN/R/R_RERI.AP.S_retro.r
CGEN/R/R_additiveTest.r
CGEN/R/R_additiveTest.small.r
CGEN/R/R_getLogLike.mat.r
CGEN/R/R_getRR.general.r
CGEN/R/R_getZ.datX.general.r
CGEN/R/R_getZ.dom.r
CGEN/R/R_getZ.general.r
CGEN/R/R_logLikBinom.add.reparam.general.r
CGEN/R/R_logLikBinom.indep.add.reparam3.general.r
CGEN/R/R_logLikBinom.indep.r
CGEN/R/R_logit.r
CGEN/R/R_makeBetaTable.general.r
CGEN/R/R_match.order.r
CGEN/R/R_multiGrep.r
CGEN/R/R_myConvertLevel.r
CGEN/R/R_myDummyVar.r
CGEN/R/R_myDummyVar3.r
CGEN/R/R_myInteractMatrix2.r
CGEN/R/R_myOR.CI3.r
CGEN/R/R_mySnp.logistic2.r
CGEN/R/R_ro.th.small4.indep2.r
CGEN/R/R_scoreTest.general9.r
CGEN/R/R_scoreTest.small.logit5.max.indep6.r
CGEN/R/R_scoreTest.small.logit5.max.r
CGEN/R/R_strCombine2.r
CGEN/R/R_variablePrep2.r
CGEN/R/additive.test.R CGEN/R/getMatchedSets.R CGEN/R/score.test.R CGEN/R/snp_matched.R CGEN/R/source.SCORE.functions.R CGEN/R/wga.R CGEN/R/wga_GbyE.R CGEN/R/wga_GbyE_print.R CGEN/R/wga_glu.R CGEN/R/wga_impute.R CGEN/R/wga_plot.R CGEN/R/wga_read.R CGEN/R/wga_stat.R CGEN/R/wga_stream.GxE.R CGEN/R/wga_stream.R CGEN/R/wga_util.R
CGEN/build
CGEN/build/vignette.rds
CGEN/data
CGEN/data/LocusMapData.txt
CGEN/data/Xdata.txt
CGEN/inst
CGEN/inst/doc
CGEN/inst/doc/vignette.R
CGEN/inst/doc/vignette.Rnw
CGEN/inst/doc/vignette.pdf
CGEN/inst/doc/vignette_GxE.R
CGEN/inst/doc/vignette_GxE.Rnw
CGEN/inst/doc/vignette_GxE.pdf
CGEN/inst/sampleData
CGEN/inst/sampleData/LocusMapData.txt
CGEN/inst/sampleData/SNPdata.rda
CGEN/inst/sampleData/Xdata.txt
CGEN/inst/sampleData/geno_data.ldat.gz
CGEN/inst/sampleData/geno_data.tfam
CGEN/inst/sampleData/geno_data.tped.gz
CGEN/inst/sampleData/geno_imputed.txt.gz
CGEN/inst/sampleData/pheno.txt
CGEN/inst/sampleData/subjects_imputed.txt
CGEN/man
CGEN/man/CGEN.Rd CGEN/man/GxE.scan.Rd CGEN/man/GxE.scan.combine.Rd CGEN/man/GxE.scan.partition.Rd CGEN/man/LocusMapData.Rd CGEN/man/QQ.plot.Rd CGEN/man/Xdata.Rd CGEN/man/additive.test.Rd CGEN/man/chromosome.plot.Rd CGEN/man/getMatchedSets.Rd CGEN/man/getSummary.Rd CGEN/man/getWaldTest.Rd CGEN/man/locusMap.list.Rd CGEN/man/pheno.list.Rd CGEN/man/printEffects.Rd CGEN/man/snp.effects.Rd CGEN/man/snp.effects.plot.Rd CGEN/man/snp.list.Rd CGEN/man/snp.logistic.Rd CGEN/man/snp.matched.Rd CGEN/man/snp.score.Rd CGEN/man/subject.list.Rd
CGEN/src
CGEN/src/Additive.c
CGEN/src/CML.c
CGEN/src/ccl.c
CGEN/src/csclust.f
CGEN/src/fsclust.c
CGEN/src/hcl.c
CGEN/src/pmatch.c
CGEN/src/score.c
CGEN/vignettes
CGEN/vignettes/vignette.Rnw
CGEN/vignettes/vignette_GxE.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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