CGEN: An R package for analysis of case-control studies in genetic epidemiology
Version 3.12.1

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

AuthorSamsiddhi Bhattacharjee, Nilanjan Chatterjee, Summer Han and William Wheeler
Bioconductor views Clustering MultipleComparisons SNP
Date of publicationNone
MaintainerWilliam Wheeler <wheelerb@imsweb.com>
LicenseGPL-2 + file LICENSE
Version3.12.1
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CGEN")

Popular 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...
GxE.scan: GxE analysis for an array of SNPs
GxE.scan.partition: Creates GxE.scan job files for a computing cluster
QQ.plot: QQ plot
snp.list: List to describe the genotype data
snp.logistic: Logistic regression analysis for a single SNP
See all...

All man pages Function index File listing

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

Functions

CGEN Man page
GC.adj.pvalues Source code
GxE.call.1 Source code
GxE.scan Man page Source code
GxE.scan.1 Source code
GxE.scan.1_2 Source code
GxE.scan.2 Source code
GxE.scan.3 Source code
GxE.scan.3a Source code
GxE.scan.4 Source code
GxE.scan.combine Man page Source code
GxE.scan.genfile Source code
GxE.scan.jobsFile Source code
GxE.scan.partition Man page Source code
GxE.setup.1 Source code
GxE.setup.1_2 Source code
GxE.setup.2 Source code
GxE.setup.3 Source code
GxE.setup.3a Source code
GxE.setup.4 Source code
LocusMapData Man page
Manhattan.plot Man page Source code
Modified_Wald_Test Source code
OR.getTitle Source code
OR.given.E Source code
OR.plot.main Source code
OR.plot.type Source code
OR.plot.type.method Source code
OR_add.LT Source code
OR_add.LT.tmp Source code
Pdg.xs.strat.dom Source code
QQ.plot Man page Source code
QQ.plot2 Source code
QQ.plot_old0 Source code
RERI.AP.S Source code
RERI.AP.S.small Source code
RERI.AP.S_retro Source code
SAS2Format Source code
UML_CML_GxE_parms Source code
Xdata Man page
addColumn Source code
addInterVars Source code
addIntercept Source code
addLineSegments Source code
addMissingSNPs Source code
additive.test Man page Source code
additiveTest Source code
additiveTest.small Source code
applyFormulas Source code
apply_zero.vars Source code
blockDiag Source code
callGLM Source code
callOS Source code
ccmatch Source code
changeAlleles Source code
changeGenotypes Source code
changeLevels.var Source code
changeStr.names Source code
changeStrata Source code
check.GLU Source code
check.PLINK Source code
check.file.list Source code
check.files Source code
check.include.snps Source code
check.list.vec.char Source code
check.locusMap.list Source code
check.pheno.list Source code
check.snp.list Source code
check.subject.list Source code
check.subsetData.list Source code
check.temp.list Source code
check.vec Source code
check.vec.char Source code
check.vec.num Source code
checkBaseModel Source code
checkDelimiter Source code
checkForConstantVar Source code
checkForSep Source code
checkPheno.vars Source code
checkTryError Source code
checkVars Source code
chrm.plot.colors Source code
chrm.plot.legend Source code
chrm.plot.main Source code
chrm.plot.pch Source code
chrm.plot.ylim Source code
closeFile Source code
convertParams3 Source code
create.formula Source code
createDummy Source code
createScript Source code
crossTab Source code
dat2rda Source code
debug.time Source code
default.list Source code
dsgnMat Source code
effScoreVar_small Source code
effScoreVar_small.split.indep2 Source code
effScoreVar_small.split2 Source code
effects.init Source code
exportSAS Source code
extract.SNP.file Source code
extract.SNP.vec Source code
extract.SNPinfo.vec Source code
extractByStr Source code
extractEst Source code
extractVar.general Source code
extract_UML.CML Source code
factorVars Source code
findRoot.optim.binary Source code
findRoot.optim.binary2 Source code
freqCounts.var Source code
gene.getOrder Source code
gene.plot Source code
gene.plot.colors Source code
gene.plot.main Source code
gene.transform.loc Source code
genfile.list Source code
genfile.vec Source code
get.EB.A_matrix Source code
get.in.miss Source code
get.nsnps.vec Source code
getAllVars Source code
getAllVars.pheno Source code
getBetaObject Source code
getCI Source code
getColNumber Source code
getColors Source code
getColsFromCharVec Source code
getColumns Source code
getCommandArg Source code
getCov12Object Source code
getCovObject Source code
getData.1 Source code
getDelimiter Source code
getDesignMatrix Source code
getEstCov Source code
getExtremeSubs Source code
getFID Source code
getFigs Source code
getFileDelim Source code
getFileHeader Source code
getFilePtr Source code
getFilePtr.genoFile Source code
getFileType Source code
getFormulas Source code
getGenoCounts Source code
getGenoStats Source code
getIds.file Source code
getIdsFromFile Source code
getInheritanceVec Source code
getInteractions Source code
getLims Source code
getLinearComb.var Source code
getListName Source code
getLocusMap Source code
getLoglike.glm Source code
getLoglike.mat Source code
getMAF Source code
getMAF.control Source code
getMatchedSets Man page Source code
getModelData Source code
getNames Source code
getNcols Source code
getNextObs Source code
getNextObs.stream Source code
getNrows Source code
getNumGenoVec Source code
getOR.CI Source code
getORfromLOR Source code
getOrder Source code
getPermutation Source code
getPermutation.strata Source code
getPheno.file Source code
getPheno.info Source code
getPhenoData Source code
getPhenoGeno.ids Source code
getPhenoGeno.stream Source code
getRR.general Source code
getRead.n Source code
getRow1.omitN Source code
getSASData Source code
getSNPinfo.vec Source code
getSNPsToInclude Source code
getSnpLoadList Source code
getSnpNames Source code
getSubIds.genoFile Source code
getSubjIds Source code
getSubject.vec Source code
getSubsToInclude Source code
getSubsetDataVars Source code
getSummary Man page Source code
getSummary.main Source code
getTempfile Source code
getUniqueChrm Source code
getUniqueVarName Source code
getValue.cvec Source code
getVarNames Source code
getVarNames.int Source code
getVarNames.snp Source code
getVecFromStr Source code
getWaldTest Man page Source code
getXBeta Source code
getZ.datX.general Source code
getZ.dom Source code
getZ.general Source code
ginfo.GLU Source code
glu.LD.snps Source code
glu.SNP_bins Source code
glu.commonSNPs Source code
glu.create_ped Source code
glu.extract Source code
glu.getCounts Source code
glu.ginfo Source code
glu.ldMatrix Source code
glu.mergeAlleles Source code
glu.mergePhenoGeno Source code
glu.nBins Source code
glu.partition Source code
glu.qcsummary Source code
glu.r2 Source code
glu.renameAlleles Source code
glu.snps_in_genes Source code
glu.transform Source code
her2.log Source code
heterTest Source code
impute.R2.GLU.file Source code
impute.R2.file Source code
impute.find_files Source code
impute.get_SNP Source code
impute.get_data Source code
impute.get_genoVec Source code
impute.get_probVecs Source code
impute.get_value Source code
impute.get_value.str Source code
impute.get_vec Source code
impute.gmodel Source code
impute.maxProbGeno Source code
impute.mergePhenoGeno Source code
impute.toLDAT.file Source code
impute.toLDAT.str Source code
impute.toTPED.file Source code
impute.toTPED.str Source code
inflationFactor Source code
info.small.add2 Source code
info.small.standard Source code
info.small_probit Source code
initDataFrame Source code
intersectSubIds Source code
likelihoodRatio Source code
likelihoodRatio.main Source code
load.impute2 Source code
loadData Source code
loadData.stream Source code
loadData.table Source code
loadData.type1 Source code
loadFile Source code
locusMap.list Man page
logLikBinom.add.reparam.general Source code
logLikBinom.indep Source code
logLikBinom.indep.add.reparam3.general Source code
logistic Source code
logistic.dsgnMat Source code
logistic.vnames Source code
logit Source code
loglikeAndRank Source code
makeBetaTable.general Source code
makeCI.nice Source code
makeVector Source code
match.order Source code Source code Source code
matchNames Source code
matrix2rda Source code
matrixDivideVec Source code
matrixMultVec Source code
mergeData Source code
mergePhenoGeno Source code
meta.EB Source code
meta.GxE Source code
meta.fixed Source code
multiGrep Source code Source code
myAR.E Source code
myAR.E2 Source code
myAR.G Source code
myAR.G2 Source code
myCbind Source code
myConvertLevel Source code Source code
myDummyVar Source code
myDummyVar3 Source code Source code
myExpectedGenotype2 Source code
myInteractMatrix2 Source code Source code
myInterval Source code
myMatrixPlot Source code
myOR.CI3 Source code Source code
myPasteCols Source code
myPercent Source code Source code
myPlot_OR_E Source code
myPlot_genScoreCompare Source code
myProcess.myStrat.inter.OR.CI4 Source code
mySnp.logistic2 Source code
myStrat.inter.OR.CI4 Source code
myStratOR.big Source code
myStrataVar Source code
mylog Source code
mylog2 Source code
myprintVars Source code
myrmvnorm Source code
nnmatch Source code
normVarNames Source code
nsnps.genoFile Source code
orderSNP Source code
orderVars Source code
outNames.cov Source code
outNames.cov2 Source code
outNames.me Source code
pair.match Source code
parse.vec Source code
parseDelimVec Source code
partialDeriv.P.betas Source code
pheno.addFormula Source code
pheno.list Man page
pheno.removeMiss Source code
pipe.genoFile.GLU Source code
populPrev Source code
populPrev2 Source code
possibleComb Source code Source code
postEps.small Source code
powerCount Source code
print.additive.test Source code
print.score.test Source code
print.score.wald Source code
print.snp.effects Source code
print.snp.effects.method Source code
print.snp.logistic Source code
print.snp.matched Source code
printEffects Man page Source code
probit.retro Source code
pvalue.normal Source code
rank.trunc.prod Source code
readFile.gz2 Source code
readFile.gzip3 Source code
readFile.type2 Source code
readFile.zip2 Source code
readTable Source code
read_C_GZ_file Source code
read_tped Source code
recode.geno Source code
removeLeading0 Source code
removeMiss Source code
removeMiss.vars Source code
removeOrKeepCols Source code
removeOrKeepRows Source code
removeWhiteSpace Source code
renameVar Source code
rep.cols Source code
rep.mat Source code
rep.rows Source code
replaceStr.list Source code
replaceStr.var Source code
riskAdd_LT Source code
riskAdd_LT2 Source code
riskAdd_LT3 Source code
riskAdd_LT_general Source code
ro.th.small4.indep.tmp Source code
ro.th.small4.indep2 Source code
ro.th.small4.tmp Source code
sMatrix.logistic Source code
save.plot Source code
scan.UML_CML Source code
scan.change.tab Source code
scan.check.transform Source code
scan.coxph Source code
scan.error Source code
scan.file Source code
scan.include.snps Source code
scan.lin_log Source code
scan.linear Source code
scan.logistic Source code
scan.stream Source code
scanFile Source code
scanNextObs Source code
score.logReg Source code
score.test Source code
score.wald Source code
scoreTest.general9 Source code
scoreTest.small.logit5.max Source code
scoreTest.small.logit5.max.indep6 Source code
set.plot Source code
setDevice Source code
setLists Source code
setPhenoList Source code
setUp.snp.list.stream Source code
setUp.stream Source code
setUpSummary Source code
setup.coxph Source code
setup.lin_log Source code
setup.linear Source code
setup.logistic Source code
snp.ccl.main Source code
snp.delete.files Source code
snp.effects Man page Source code
snp.effects.plot Man page Source code
snp.hcl.main Source code
snp.list Man page
snp.logistic Man page Source code
snp.main Source code
snp.matched Man page Source code
snp.scan.logistic Source code
snp.score Man page Source code
snpPlot3 Source code
snps.genoFile.GLU Source code
sort2D Source code
standardize.z Source code
strCombine2 Source code Source code
strataMatrix Source code
subject.list Man page
subs.genoFile.GLU Source code
subsetData.list Source code
subsetData.var Source code
summary.snp.logistic Source code
summary.snp.matched Source code
swap2cols.cov Source code
table2Format Source code
threshold.trunc.prod Source code
transCall.genoFile.GLU Source code
transform.genoFile Source code
transform.genoFile.GLU Source code
transform.genoFile.PLINK Source code
transform.loc Source code
unadjustedGLM.counts Source code
unfactor Source code
unfactor.all Source code
update.snp.list Source code
update.snpNames Source code
variablePrep2 Source code
variablePrep3 Source code
wald.test Source code
wald.weight.indep Source code
waldTest.main Source code
writeOut Source code
writeSnpLines Source code
writeTable Source code
writeVec Source code
writeVecToFile Source code

Files

DESCRIPTION
LICENSE
NAMESPACE
NEWS
R
R/Modified_Wald_Test_Sandwich_v3.R
R/R_Pdg.xs.strat.dom.r
R/R_RERI.AP.S.r
R/R_RERI.AP.S.small.r
R/R_RERI.AP.S_retro.r
R/R_additiveTest.r
R/R_additiveTest.small.r
R/R_getLogLike.mat.r
R/R_getRR.general.r
R/R_getZ.datX.general.r
R/R_getZ.dom.r
R/R_getZ.general.r
R/R_logLikBinom.add.reparam.general.r
R/R_logLikBinom.indep.add.reparam3.general.r
R/R_logLikBinom.indep.r
R/R_logit.r
R/R_makeBetaTable.general.r
R/R_match.order.r
R/R_multiGrep.r
R/R_myConvertLevel.r
R/R_myDummyVar.r
R/R_myDummyVar3.r
R/R_myInteractMatrix2.r
R/R_myOR.CI3.r
R/R_mySnp.logistic2.r
R/R_ro.th.small4.indep2.r
R/R_scoreTest.general9.r
R/R_scoreTest.small.logit5.max.indep6.r
R/R_scoreTest.small.logit5.max.r
R/R_strCombine2.r
R/R_variablePrep2.r
R/additive.test.R
R/getMatchedSets.R
R/score.test.R
R/snp_matched.R
R/source.SCORE.functions.R
R/wga.R
R/wga_GbyE.R
R/wga_GbyE_print.R
R/wga_glu.R
R/wga_impute.R
R/wga_plot.R
R/wga_read.R
R/wga_stat.R
R/wga_stream.GxE.R
R/wga_stream.R
R/wga_util.R
build
build/vignette.rds
data
data/LocusMapData.txt
data/Xdata.txt
inst
inst/doc
inst/doc/vignette.R
inst/doc/vignette.Rnw
inst/doc/vignette.pdf
inst/doc/vignette_GxE.R
inst/doc/vignette_GxE.Rnw
inst/doc/vignette_GxE.pdf
inst/sampleData
inst/sampleData/LocusMapData.txt
inst/sampleData/SNPdata.rda
inst/sampleData/Xdata.txt
inst/sampleData/geno_data.ldat.gz
inst/sampleData/geno_data.tfam
inst/sampleData/geno_data.tped.gz
inst/sampleData/geno_imputed.txt.gz
inst/sampleData/pheno.txt
inst/sampleData/subjects_imputed.txt
man
man/CGEN.Rd
man/GxE.scan.Rd
man/GxE.scan.combine.Rd
man/GxE.scan.partition.Rd
man/LocusMapData.Rd
man/QQ.plot.Rd
man/Xdata.Rd
man/additive.test.Rd
man/chromosome.plot.Rd
man/getMatchedSets.Rd
man/getSummary.Rd
man/getWaldTest.Rd
man/locusMap.list.Rd
man/pheno.list.Rd
man/printEffects.Rd
man/snp.effects.Rd
man/snp.effects.plot.Rd
man/snp.list.Rd
man/snp.logistic.Rd
man/snp.matched.Rd
man/snp.score.Rd
man/subject.list.Rd
src
src/Additive.c
src/CML.c
src/ccl.c
src/csclust.f
src/fsclust.c
src/hcl.c
src/pmatch.c
src/score.c
vignettes
vignettes/vignette.Rnw
vignettes/vignette_GxE.Rnw
CGEN documentation built on May 20, 2017, 10:14 p.m.

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