API for GGtools
software and data for analyses in genetics of gene expression

Global functions
.combine2	Source code
.mapSnps2Genes	Source code
.pifdrA	Source code
.pifdrB	Source code
.summarize	Source code
.topFeats	Source code Source code
.transTab	Source code
.updateKfeats	Source code
.validEQA	Source code
All.cis	Man page
All.cis.chr	Source code
All.cis.eQTLs	Man page
All.cis.legacy	Source code
All.cis.mchr	Source code
CisConfig-class	Man page
EqAppr-class	Man page
GGtools	Man page
GGtools-package	Man page
SSgen	Man page
SSgen,CisConfig-method	Man page
SSgen<-	Man page
SSgen<-,CisConfig,function-method	Man page
SnpMatrixCisToSummex	Source code
TabixFile	Man page
TransConfig-class	Man page
[,eqtlTestsManager,ANY,ANY,ANY-method	Man page
add878	Man page Source code
addcadd	Source code
addgwhit	Man page Source code
allBinnedPredictions	Source code
allCalibProportions	Source code
allSigCis-class	Man page
allTruePos	Source code
appraise	Man page Source code
b1	Man page
b2	Man page
batchsize	Man page
batchsize,TransConfig-method	Man page
batchsize<-	Man page
batchsize<-,TransConfig,integer-method	Man page
best.cis.eQTLs	Man page Source code
best.trans.eQTLs	Man page Source code
bindgwava	Man page
bindmaf	Man page
bindmaf.legacy	Source code
bindmaf.simple	Source code
bindmafAll	Man page
bindprops	Source code
binnedQQ	Man page Source code
binqq	Man page Source code
buildApprRes	Source code
buildConfList	Man page Source code
buildEqAppr	Source code
calfig	Man page
calfig,EqAppr,character-method	Man page
ceuCon19	Source code
cgff2dt	Man page Source code
chkeman	Source code Source code
chrFilter	Man page Source code
chrnames	Man page
chrnames,CisConfig-method	Man page
chrnames<-	Man page
chrnames<-,CisConfig,character-method	Man page
chromsUsed	Man page
chromsUsed,mcwBestCis-method	Man page
cis.FDR.filter.SNPcentric	Man page Source code
cis.FDR.filter.SNPcentric.complete	Man page Source code
cis.FDR.filter.best	Man page
cis.FDR.filter.best.old	Source code
cisAssoc	Man page Man page Source code
cisRun-class	Man page
cisScores	Man page Source code
cisZero	Source code
ciseqByCluster	Man page Source code
cleanup_transff	Source code
collectBest	Man page Source code
collectFiltered	Man page Source code
comlist	Source code
concatCis	Man page Source code
convertCis	Source code
dtToAppr	Source code
eqBox	Man page Source code
eqDesc	Man page
eqsens_dt	Man page Source code
eqtlEstimates	Man page Source code
eqtlEstimatesManager-class	Man page
eqtlTests	Man page Source code
eqtlTests.me	Man page Source code
eqtlTests.meText	Source code
eqtlTests2	Source code
eqtlTestsManager-class	Man page
eqtlscan	Source code
estimates	Man page
estimates,CisConfig-method	Man page
estimates<-	Man page
estimates<-,CisConfig,logical-method	Man page
ex	Man page
exFilter	Man page
exFilter,CisConfig-method	Man page
exFilter<-	Man page
exFilter<-,CisConfig,function-method	Man page
excludeRadius	Man page
excludeRadius,CisConfig-method	Man page
excludeRadius<-	Man page Man page
excludeRadius<-,CisConfig,integer-method	Man page
excludeRadius<-,CisConfig,integerOrNULL-method	Man page
extraProps	Man page
extraProps,CisConfig-method	Man page
extraProps<-	Man page
extraProps<-,CisConfig,function-method	Man page
fdr	Man page Source code
ffSnpSummary.legacy	Source code
filtgen.maf.dist	Man page Source code
folderStem	Man page
folderStem,CisConfig-method	Man page
folderStem<-	Man page
folderStem<-,CisConfig,character-method	Man page
fplot	Source code
fullparse	Source code
fullreport	Man page
fullreport,mcwBestCis,character-method	Man page
fullreport,mcwBestCis,missing-method	Man page
gbufsize	Man page
gbufsize,TransConfig-method	Man page
gbufsize<-	Man page
gbufsize<-,TransConfig,integer-method	Man page
gchrpref	Man page
gchrpref,CisConfig-method	Man page
gchrpref<-	Man page
gchrpref<-,CisConfig,character-method	Man page
geneApply	Man page
geneApply,CisConfig-method	Man page
geneApply<-	Man page
geneApply<-,CisConfig,function-method	Man page
geneIndcol	Man page Source code
geneNames	Man page Source code
geneannopk	Man page
geneannopk,CisConfig-method	Man page
geneannopk<-	Man page
geneannopk<-,CisConfig,character-method	Man page
genemodel	Source code
genome	Man page
genome,CisConfig-method	Man page
genome<-	Man page
genome<-,CisConfig,character-method	Man page
genome<-,CisConfig-method	Man page
get.dffits	Source code
getAUCs	Source code
getAll	Man page Source code
getAsSlicedData	Source code
getBest	Man page Source code
getCall	Man page Source code
getCisMap	Man page Source code
getFDR	Source code
getModnames,EqAppr-method	Man page
getNodeNames	Source code
getPruned,EqAppr-method	Man page
getSens,EqAppr-method	Man page
getUnpruned,EqAppr-method	Man page
get_probechunks	Source code
getall	Source code
getsfp	Source code
gffprocess	Man page Source code
gwSnpScreenResult-class	Man page
gwSnpTests	Man page
gwSnpTests,formula,smlSet,missing-method	Man page
gwSnpTests,formula,smlSet-method	Man page
hg19.si.df	Man page
hmm878	Man page
inflammFilter	Man page Source code
initialize	Man page
initialize,CisConfig-method	Man page
intersectSnps	Source code
ivector	Source code
keepMapCache	Man page
keepMapCache,CisConfig-method	Man page
keepMapCache<-	Man page
keepMapCache<-,CisConfig,logical-method	Man page
lgeu	Man page
locusNames	Man page Source code
makeCommonSNPs	Source code
makeSeqinfo	Source code
maxAtFDR	Source code
mcwAllCis-class	Man page
mcwBestCis-class	Man page
meqtlTests	Man page Source code
meta.All.cis.eQTLs	Man page Source code
meta.best.cis.eQTLs	Man page Source code
meta.bindmaf	Man page Source code
meta.richNull	Man page Source code
meta.transScores	Man page
minchisqAtFDR	Source code
mtransScores	Man page
nperm	Man page
nperm,CisConfig-method	Man page
nperm<-	Man page
nperm<-,CisConfig,integer-method	Man page
nthScores	Man page Source code
optAUC	Source code
parseVCFrec	Source code
pifdr	Man page Source code
pifdr.old	Source code
plot,gwSnpScreenResult,character-method	Man page
plotsens	Man page Source code
probesManaged	Man page Source code
probesWeqtl	Source code
procnames	Source code
pullHits	Source code
qqhex	Man page Source code
radius	Man page
radius,CisConfig-method	Man page
radius<-	Man page
radius<-,CisConfig,integer-method	Man page
reduceGenes	Source code
relocate	Source code
restrictProbesToChrom	Source code
rhs	Man page
rhs,CisConfig-method	Man page
rhs<-	Man page Man page
rhs<-,CisConfig,formula-method	Man page
rhs<-,CisConfig,function-method	Man page
richNull	Man page Source code
sampsInVCF	Man page Source code
schrpref	Man page
schrpref,CisConfig-method	Man page
schrpref<-	Man page
schrpref<-,CisConfig,character-method	Man page
scoresCis	Man page Source code
sensFromDT	Source code
sensanal	Man page
sensanal,sensiCisInput,numeric-method	Man page
sensiCisInput-class	Man page
sensiCisOutput-class	Man page
shortfac	Man page
shortfac,CisConfig-method	Man page
shortfac<-	Man page
shortfac<-,CisConfig,integer-method	Man page
show	Man page
show,ApprRes-method	Man page
show,CisConfig-method	Man page
show,EqAppr-method	Man page
show,TransConfig-method	Man page
show,allCigCis-method	Man page
show,allSigCis-method	Man page
show,cisMap-method	Man page
show,cwBestCis-method	Man page
show,eqtlTestsManager-method	Man page
show,gwSnpScreenResult,character-method	Man page
show,gwSnpScreenResult-method	Man page
show,mcwAllCis-method	Man page
show,mcwBestCis-method	Man page
show,metaVCF-method	Man page
show,sensiCisInput-method	Man page
show,sensiCisOutput-method	Man page
show,transManager-method	Man page
simpleTiling	Man page Source code
smFilter	Man page
smFilter,CisConfig-method	Man page
smFilter<-	Man page
smFilter<-,CisConfig,function-method	Man page
smchrpref	Man page
smchrpref,CisConfig-method	Man page
smchrpref<-	Man page
smchrpref<-,CisConfig,character-method	Man page
smpack	Man page
smpack,CisConfig-method	Man page
smpack<-	Man page
smpack<-,CisConfig,character-method	Man page
snpannopk	Man page
snpannopk,CisConfig-method	Man page
snpannopk<-	Man page
snpannopk<-,CisConfig,character-method	Man page
snpchr	Man page
snpchr,TransConfig-method	Man page
snpchr<-	Man page
snpchr<-,TransConfig,character-method	Man page
snplocsDefault	Man page Source code
snpsCisToGenes	Source code
snpsManaged	Man page Source code
snvsOnly	Source code
strMultPop	Man page
textAndSlice	Source code
topFeats	Man page
topFeats,probeId,eqtlTestsManager-method	Man page
topFeats,rsid,eqtlTestsManager-method	Man page
topGenes	Man page Source code
topKfeats	Source code
topScores	Man page Source code
topSnps	Man page
topSnps,gwSnpScreenResult-method	Man page
tr1_obs	Man page
tr1_perm	Man page
transManager-class	Man page
transScores	Man page
transScores.legacy	Man page
transTab	Man page
transTab,transManager,character-method	Man page
transTab,transManager,missing-method	Man page
transeqByChrom	Man page Source code
transeqByCluster	Man page Source code
trimSnps	Source code
tscan2df	Source code
tscan2gr	Source code
unified.col.summary	Source code
unquote	Source code
updateKfeats	Source code
update_fdr_filt	Man page Source code
vcf2sm	Man page
vcf2sm,TabixFile,GRanges,integer-method	Man page
waldtests	Source code