GGtools: software and data for analyses in genetics of gene expression
Version 5.12.0

software and data for analyses in genetics of gene expression and/or DNA methylation

Browse man pages Browse package API and functions Browse package files

AuthorVJ Carey <stvjc@channing.harvard.edu>
Bioconductor views GeneExpression GeneticVariability Genetics SNP
Date of publicationNone
MaintainerVJ Carey <stvjc@channing.harvard.edu>
LicenseArtistic-2.0
Version5.12.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GGtools")

Man pages

All.cis: functions that compute score tests for all SNP cis to genes,...
appraise: appraisal for eQTL prediction models
b1: mcwBestCis instances, integrative analysis output containers...
best.cis.eQTLs: collect genewise best scoring eQTL
best.trans.eQTLs: collect strongest trans SNP-gene associations in a buffer of...
bindmaf: bind testing metadata to a best.cis.eQTLs result
cgff2dt: translate the GFF3 from a ciseqByCluster/processgff output...
cisAssoc: test for variant-expression associations in cis, using VCF
CisConfig-class: Class '"CisConfig"'
ciseqByCluster: end-to-end cluster-based cis-eQTL search, and allied...
cisRun-class: Class '"cisRun"'
collectBest: given a collection of All.cis outputs (cisRun instances)...
concatCis: combine a list of cisRun instances to a single instance
EqAppr-class: Class '"EqAppr"'
eqBox: descriptive plot of expression against genotype for cisAssoc...
eqsens_dt: support for sensitivity analyses related to eQTL enumerations
eqtlTests: compute association statistics between all probes and SNP in...
eqtlTestsManager-class: Class '"eqtlTestsManager"'
eqtlTests.me: use MatrixEQTL computations and statistics as a back end to...
ex: ExpressionSet instance for illustrating integrative smlSet...
getCisMap: create, using Bioconductor annotation resources, a structure...
gffprocess: transform a collection of gff3 into a single tabix-indexed...
GGtools-package: software and data for analyses in genetics of gene expression
gwSnpTests: execute a series of tests for association between genotype...
hmm878: labeled GRanges with ChromHMM chromatin states for GM12878
pifdr: utility for computing plug-in FDR
qqhex: obtain qqplot coordinates for the specific case of comparing...
richNull: bind metadata concerning SNP allele frequency and other...
sampsInVCF: enumerate samples available in a VCF file
scoresCis: visualize a gene model with cis-eQTL association scores (-log...
sensanal: Summarize information from a collection of eQTL searches for...
sensiCisInput-class: Class '"sensiCisInput"'
sensiCisOutput-class: Class '"sensiCisOutput"'
simpleTiling: create a GRanges with a tiling of the human genome
snplocsDefault: name the default SNPlocs.Hsapiens.dbSNP.* package
strMultPop: serialization of a table from Stranger's multipopulation eQTL...
TransConfig-class: Class '"TransConfig"'
transeqByCluster: convenience functions for trans-eQTL testing
transManager-class: Class '"transManager"'
transScores: obtain the top trans associations for each SNP in an smlSet
transTab: tabulate results of transScores run
vcf2sm: generate a SnpMatrix instance on the basis of a VCF (4.0)...

Functions

All.cis Man page
All.cis.chr Source code
All.cis.eQTLs Man page Source code
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.cis.eQTLs.chr Source code
best.cis.eQTLs.mchr Source code
best.trans.eQTLs Man page Source code
bestInStratum Source code
bindGeneRanges2mgr Source code
bindSnpRanges2mgr 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 Source code Source code
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 Source code
cis.FDR.filter.best.old Source code
cisAssoc Man page Man page Source code
cisFilter Source code
cisRun-class Man page
cisScores Man page Source code
cisZero Source code Source code
ciseqByCluster Man page Source code
cleanup Source code
cleanup_transff Source code
collectBest Man page Source code
collectFiltered Man page Source code
combine2 Source code Source code
comlist Source code
concatCis Man page Source code
convertCis Source code
crg2gr Source code
dtToAppr Source code
eqBox Man page Source code
eqDesc Man page Source code
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 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
genePosition 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
hns Source code
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
mapSnps2Genes 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.all.cis.eQTLs.chr Source code
meta.all.cis.eQTLs.mchr Source code
meta.best.cis.eQTLs Man page Source code
meta.best.cis.eQTLs.chr Source code
meta.best.cis.eQTLs.mchr Source code
meta.bindmaf Man page Source code
meta.richNull Man page Source code
meta.transScores Man page Source code
minchisqAtFDR Source code
mtransScores Man page Source code
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
pifdrA Source code
pifdrB 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
queryCrg 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
scoredist Source code
scoresCis Man page Source code
scoresInStratum Source code
sensFromDT Source code
sensanal Man page
sensanal,sensiCisInput,numeric-method Man page
sensiCisInput-class Man page
sensiCisOutput-class Man page
sgf Source code
sgf.slow Source code
sgf.unsafe Source code
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
summarize Source code
sym2id Source code
textAndSlice Source code
topFeats Man page Source code Source code
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 Source code
tr1_perm Man page Source code
transManager-class Man page
transScores Man page Source code
transScores.legacy Man page Source code
transTab Man page Source code
transTab,transManager,character-method Man page
transTab,transManager,missing-method Man page
transeqByChrom Man page Source code
transeqByCluster Man page Source code
treloc Source code
trimSnps Source code
tscan2df Source code
tscan2gr Source code
unified.col.summary Source code
unquote Source code
updateKfeats Source code Source code
update_fdr_filt Man page Source code
validEQA Source code
vcf2sm Man page
vcf2sm,TabixFile,GRanges,integer-method Man page
waldtests Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AllClasses.R
R/AllGenerics.R
R/Eqappr.R
R/alleq.R
R/basicappraise.R
R/best.trans.eQTLs.R
R/bindmaf.R
R/binqq.R
R/cisConfig.R
R/cisEqTools.R
R/cisa.R
R/eqME.R
R/eqtlEstimates.R
R/eqtlTests.R
R/fdr.all.cis.R
R/getFDR.R
R/gffprocess.R
R/gwSnpTests.R
R/harvest.R
R/managers.R
R/meta.R
R/meta.all.R
R/meta.transScores.R
R/modutils.R
R/pifdr.R
R/pureSensSoft.R
R/relocate.R
R/scan.R
R/scoredist.R
R/seqinfo.R
R/snplocsDefault.R
R/snpsCisToGenes.R
R/summInfra.R
R/thinclass.R
R/topFeats.R
R/topSnps.R
R/transutils.R
R/vcfutils.R
README
TODO.txt
build
build/vignette.rds
data
data/b1.rda
data/b2.rda
data/datalist
data/eset.rda
data/hg19.si.df.rda
data/hmm878.rda
data/lgeu.rda
data/strMultPop.rda
inst
inst/CITATION
inst/cloud
inst/cloud/ciseqByCluster.R
inst/cloud/newtest.R
inst/doc
inst/doc/GGtools.R
inst/doc/GGtools.Rnw
inst/doc/GGtools.pdf
inst/extpacksupp
inst/extpacksupp/DESCRIPTION.proto
inst/extpacksupp/zzz.R
inst/hapmap
inst/hapmap/relationships_w_pops_051208.txt
inst/hapmap/smallc20CEU.txt.gz
inst/hapmap/src.rel.txt
inst/oldRsrc
inst/oldRsrc/X2chunk.R
inst/oldRsrc/allS4.R
inst/oldRsrc/bestCis.R
inst/oldRsrc/bindScores.R
inst/oldRsrc/cisFDR.R
inst/oldRsrc/cisSnpTests.R
inst/oldRsrc/cisgetter.R
inst/oldRsrc/clipPCs.R
inst/oldRsrc/comb.R
inst/oldRsrc/egtset.R
inst/oldRsrc/eqtlEstimates.R
inst/oldRsrc/exome_minp.R
inst/oldRsrc/externalize.R
inst/oldRsrc/feqtltests.R
inst/oldRsrc/filterCode.R
inst/oldRsrc/fullsynth.R
inst/oldRsrc/geneRanges.R
inst/oldRsrc/geneTrack.R
inst/oldRsrc/getTransScores.R
inst/oldRsrc/gwSnpScreen.R
inst/oldRsrc/interleave2cis.R
inst/oldRsrc/machutils.R
inst/oldRsrc/minp.R
inst/oldRsrc/multff.R
inst/oldRsrc/newEQTL.R
inst/oldRsrc/pcc.R
inst/oldRsrc/permEx.R
inst/oldRsrc/probeloc.R
inst/oldRsrc/regressOut.R
inst/oldRsrc/scoresInRanges.R
inst/oldRsrc/shiftRight.R
inst/oldRsrc/snp130locs.R
inst/oldRsrc/sumDirectors.R
inst/oldRsrc/zzz.R
inst/oldman
inst/oldman/GGtools-package.Rd
inst/oldman/X2chunk.Rd
inst/oldman/best.cis.eQTLs.Rd
inst/oldman/calfig.Rd
inst/oldman/cisProxScores-class.Rd
inst/oldman/cisProxScores.Rd
inst/oldman/clipPCs.Rd
inst/oldman/degnerASE01.Rd
inst/oldman/dropMonomorphies.Rd
inst/oldman/eqtlEstimatesManager-class.Rd
inst/oldman/eqtlFDRtab-class.Rd
inst/oldman/eqtlTests.Rd
inst/oldman/eqtlTestsManager-class.Rd
inst/oldman/ex6.Rd
inst/oldman/exome_minp.Rd
inst/oldman/externalize.Rd
inst/oldman/geneIndcol.Rd
inst/oldman/geneRanges.Rd
inst/oldman/genewiseFDRtab.Rd
inst/oldman/gwSnpTests.Rd
inst/oldman/hla2set.Rd
inst/oldman/hmceuB36.2021.Rd
inst/oldman/imphm2_1KG_20.Rd
inst/oldman/m20.Rd
inst/oldman/makeCommonSNPs.Rd
inst/oldman/manhPlot.Rd
inst/oldman/mkCisTransDirector.Rd
inst/oldman/mrefhap2sm.Rd
inst/oldman/multiCisDirector-class.Rd
inst/oldman/pcChooser.Rd
inst/oldman/permEx.Rd
inst/oldman/plot-methods.Rd
inst/oldman/probeLocations.Rd
inst/oldman/relocate.Rd
inst/oldman/sm2ped.Rd
inst/oldman/topSnps-methods.Rd
inst/oldman/transManager-class.Rd
inst/oldman/transScores.Rd
inst/oldman/transTab.Rd
inst/oldman/vcf2sm-methods.Rd
inst/oldman/vcf2sm.Rd
inst/parts
inst/parts/20.rda
inst/parts/21.rda
inst/provenance
inst/provenance/human
inst/provenance/human/doallgzOct17b.R
inst/provenance/human/getall.sh
inst/provenance/human/notes.txt
inst/provenance/mouse
inst/provenance/mouse/notes.txt
inst/pup
inst/pup/combn238_chr6.pup
inst/rdas
inst/rdas/ceu_21.rda
inst/rdas/ceu_22.rda
inst/scripts
inst/scripts/lkme.Rnw
inst/scripts/lkme.pdf
inst/vcf
inst/vcf/CEU.exon.2010_09.genotypes.vcf.gz
inst/vcf/CEU.exon.2010_09.genotypes.vcf.gz.tbi
inst/vcf/c20exch.vcf.gz
inst/vcf/c20exch.vcf.gz.tbi
inst/vcf/provenance.txt
inst/vcf/valid-4.0.vcf.gz
man
man/All.cis.Rd
man/CisConfig-class.Rd
man/EqAppr-class.Rd
man/GGtools-package.Rd
man/TransConfig-class.Rd
man/appraise.Rd
man/b1.Rd
man/best.cis.eQTLs.Rd
man/best.trans.eQTLs.Rd
man/bindmaf.Rd
man/cgff2dt.Rd
man/cisAssoc.Rd
man/cisRun-class.Rd
man/ciseqByCluster.Rd
man/collectBest.Rd
man/concatCis.Rd
man/eqBox.Rd
man/eqsens_dt.Rd
man/eqtlTests.Rd
man/eqtlTests.me.Rd
man/eqtlTestsManager-class.Rd
man/ex.Rd
man/getCisMap.Rd
man/gffprocess.Rd
man/gwSnpTests.Rd
man/hmm878.Rd
man/pifdr.Rd
man/qqhex.Rd
man/richNull.Rd
man/sampsInVCF.Rd
man/scoresCis.Rd
man/sensanal.Rd
man/sensiCisInput-class.Rd
man/sensiCisOutput-class.Rd
man/simpleTiling.Rd
man/snplocsDefault.Rd
man/strMultPop.Rd
man/transManager-class.Rd
man/transScores.Rd
man/transTab.Rd
man/transeqByCluster.Rd
man/vcf2sm.Rd
tests
tests/cis.R
tests/eqvgwst.R
tests/f2.fdr.rda
tests/f2.score.rda
tests/test.meqtlTests.R
tests/test.meta.trans.R
tests/testCisMap.R
tests/testTrans.R
vignettes
vignettes/GGtools.Rnw
vignettes/cpne1Brow.pdf
vignettes/ggtvig.bib
GGtools documentation built on May 20, 2017, 9:49 p.m.