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

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

Author
Samsiddhi Bhattacharjee, Nilanjan Chatterjee, Summer Han and William Wheeler
Date of publication
None
Maintainer
William Wheeler <wheelerb@imsweb.com>
License
GPL-2 + file LICENSE
Version
3.10.0

View on Bioconductor

Man pages

additive.test
A test for gene-environment interaction under an additive...
CGEN
An R package for analysis of case-control studies in genetic...
chromosome.plot
Manhattan 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
LocusMapData
Locus map data
locusMap.list
List to describe the locus map data
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...
snp.score
Score Test
subject.list
List to describe the file of subject ids
Xdata
Sample covariate and outcome data

Files in this package

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