API for ARTP
Gene and Pathway p-Values Computed using the Adaptive Rank Truncated Product

Global functions
ARTP Man page
ARTP_pathway Man page Source code
GC.adj.pvalues Source code
LOR.flip Source code
OR.getTitle Source code
OR.plot.main Source code
OR.plot.type Source code
OR.plot.type.method Source code
QQ.plot Source code
QQ.plot2 Source code
SAS2Format Source code
addColumn Source code
addInterVars Source code
addIntercept Source code
addLineSegments Source code
addMissingSNPs Source code
allele.flip Source code
appendFiles Source code
applyFormulas Source code
blockDiag Source code
cal.expect Source code
callGLM Source code
callOS Source code
changeAlleles Source code
changeGenotypes Source code
changeLevels.var Source code
changeStr.names Source code
changeStrata Source code
check.data.list Source code
check.file.list Source code
check.files Source code
check.gene.list Source code
check.group.list Source code
check.list.vec.char Source code
check.locusMap.list Source code
check.obs.list Source code
check.perm.list Source code
check.pheno.list Source code
check.snp.list Source code
check.study.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
checkDelimiter Source code
checkForConstantVar Source code
checkForSep 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
chromosome.plot Source code
closeFile Source code
combObserved.study Source code
combPerm.study Source code
combPvalue.log Source code
combVars.study Source code
combineByPathway_Kai Source code
combineTime Source code
convert.obsfile 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
effects.init Source code
exportSAS Source code
extractByStr Source code
factorVars Source code
freqCounts.var Source code
gene.getOrder Source code
gene.list Man page
gene.plot Source code
gene.plot.colors Source code
gene.plot.main Source code
gene.transform.loc Source code
geneSNPs.study Source code
geneStat.obs Source code
geneStat.perm Source code
geneStats.init Source code
gene_SNP_data Man page
genfile.list Source code
genfile.vec Source code
geno_data Man page
get.in.miss Source code
getAllVars Source code
getCI Source code
getColNumber Source code
getColors Source code
getColsFromCharVec Source code
getColumns Source code
getCommandArg Source code
getData.1 Source code
getDelimiter Source code
getDesignMatrix Source code
getEstCov Source code
getExtremeSubs Source code
getFID Source code
getFID.study Source code
getFileDelim Source code
getFileHeader Source code
getFileType Source code
getFormulas Source code
getGene.parms Source code
getGenoCounts Source code
getGenoStats Source code
getIdsFromFile Source code
getInheritanceVec Source code
getInteractions Source code
getLinearComb.var Source code
getListName Source code
getLocusMap Source code
getLoglike.glm Source code
getMAF Source code
getMAF.control Source code
getMinPerm.study Source code
getModelData Source code
getNames Source code
getNcols Source code
getNcols.study Source code
getNextObs Source code
getNperm Source code
getNperm.study Source code
getNrows Source code
getOR.CI Source code
getORfromLOR Source code
getObserved.study Source code
getObserved.vec Source code
getOrder Source code
getPermutation Source code
getPermutation.strata Source code
getPheno.info Source code
getPhenoData Source code
getRead.n Source code
getReadN.double Source code
getRow1.omitN Source code
getSASData Source code
getSNPnames.study Source code
getSnpLoadList Source code
getSnpNames Source code
getSubjIds Source code
getSubject.vec Source code
getSubsetDataVars Source code
getSummary Source code
getSummary.main Source code
getTempfile Source code
getUniqueChrm Source code
getUniqueVarName Source code
getVarNames Source code
getVarNames.int Source code
getVarNames.snp Source code
getVecFromStr Source code
getWaldTest Source code
getXBeta Source code
globalAlleles Source code
glu.SNP_bins Source code
glu.commonSNPs Source code
glu.create_ped 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
heterTest Source code
inflationFactor 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
loglikeAndRank Source code
makeVector Source code
matchNames Source code
matrix2rda Source code
matrixDivideVec Source code
matrixMultVec Source code
mergeData Source code
mergePhenoGeno Source code
meta Source code
meta.analysis Source code
meta.mima.scan Source code
meta.setup Source code
meta.update Source code
mima Source code
myrmvnorm Source code
normVarNames Source code
obs_pvalues Man page
orderSNP Source code
orderVars Source code
parse.vec Source code
perm.closeFiles Source code
perm.deleteFiles Source code
perm.getData Source code
perm.glm Source code
perm.openFiles Source code
perm.readData Source code
permReg Source code
perm_pvalues Man page
pheno.list Man page
pheno_data Man page
plot_genes Man page 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
readPermData Source code
readTable 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
runPermutations Man page Source code
save.plot Source code
scanFile Source code
scanNextObs Source code
score.logReg Source code
set.plot Source code
setDevice Source code
setUp.stream Source code
setUpSummary Source code
single.marker.test Man page Source code
snp.effects Source code
snp.effects.plot Source code
snp.list Man page
sort2D Source code
standardize.z Source code
strataMatrix Source code
subsetData.list Source code
subsetData.var Source code
subsetPermData Source code
swap2cols.cov Source code
table2Format Source code
threshold.trunc.prod 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
waldTest.main Source code
writeSnpLines Source code
writeTable Source code
writeVec Source code
writeVecToFile Source code
ARTP documentation built on May 2, 2019, 6:51 a.m.