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

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

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GGtools")
AuthorVJ Carey <stvjc@channing.harvard.edu>
Bioconductor views GeneExpression GeneticVariability Genetics SNP
Date of publicationNone
MaintainerVJ Carey <stvjc@channing.harvard.edu>
LicenseArtistic-2.0
Version5.10.1

View on Bioconductor

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

add878 Man page
addgwhit Man page
All.cis Man page
All.cis.eQTLs Man page
allSigCis-class Man page
appraise Man page
b1 Man page
b2 Man page
batchsize Man page
batchsize<- Man page
batchsize<-,TransConfig,integer-method Man page
batchsize,TransConfig-method Man page
best.cis.eQTLs Man page
best.trans.eQTLs Man page
bindgwava Man page
bindmaf Man page
bindmafAll Man page
binnedQQ Man page
binqq Man page
buildConfList Man page
calfig Man page
calfig,EqAppr,character-method Man page
cgff2dt Man page
chrFilter Man page
chrnames Man page
chrnames<- Man page
chrnames<-,CisConfig,character-method Man page
chrnames,CisConfig-method Man page
chromsUsed Man page
chromsUsed,mcwBestCis-method Man page
cisAssoc Man page
CisConfig-class Man page
ciseqByCluster Man page
cis.FDR.filter.best Man page
cis.FDR.filter.SNPcentric Man page
cis.FDR.filter.SNPcentric.complete Man page
cisRun-class Man page
cisScores Man page
collectBest Man page
collectFiltered Man page
concatCis Man page
EqAppr-class Man page
eqBox Man page
eqDesc Man page
eqsens_dt Man page
eqtlEstimates Man page
eqtlEstimatesManager-class Man page
eqtlTests Man page
[,eqtlTestsManager,ANY,ANY,ANY-method Man page
eqtlTestsManager-class Man page
eqtlTests.me Man page
estimates Man page
estimates<- Man page
estimates<-,CisConfig,logical-method Man page
estimates,CisConfig-method Man page
ex Man page
excludeRadius Man page
excludeRadius<- Man page
excludeRadius<-,CisConfig,integer-method Man page
excludeRadius<-,CisConfig,integerOrNULL-method Man page
excludeRadius,CisConfig-method Man page
exFilter Man page
exFilter<- Man page
exFilter<-,CisConfig,function-method Man page
exFilter,CisConfig-method Man page
extraProps Man page
extraProps<- Man page
extraProps<-,CisConfig,function-method Man page
extraProps,CisConfig-method Man page
fdr Man page
filtgen.maf.dist Man page
folderStem Man page
folderStem<- Man page
folderStem<-,CisConfig,character-method Man page
folderStem,CisConfig-method Man page
fullreport Man page
fullreport,mcwBestCis,character-method Man page
fullreport,mcwBestCis,missing-method Man page
gbufsize Man page
gbufsize<- Man page
gbufsize<-,TransConfig,integer-method Man page
gbufsize,TransConfig-method Man page
gchrpref Man page
gchrpref<- Man page
gchrpref<-,CisConfig,character-method Man page
gchrpref,CisConfig-method Man page
geneannopk Man page
geneannopk<- Man page
geneannopk<-,CisConfig,character-method Man page
geneannopk,CisConfig-method Man page
geneApply Man page
geneApply<- Man page
geneApply<-,CisConfig,function-method Man page
geneApply,CisConfig-method Man page
geneIndcol Man page
geneNames Man page
genome Man page
genome<- Man page
genome<-,CisConfig,character-method Man page
genome<-,CisConfig-method Man page
genome,CisConfig-method Man page
getAll Man page
getBest Man page
getCall Man page
getCisMap Man page
getModnames,EqAppr-method Man page
getPruned,EqAppr-method Man page
getSens,EqAppr-method Man page
getUnpruned,EqAppr-method Man page
gffprocess Man page
GGtools Man page
GGtools-package Man page
gwSnpScreenResult-class Man page
gwSnpTests Man page
gwSnpTests,formula,smlSet-method Man page
gwSnpTests,formula,smlSet,missing-method Man page
hg19.si.df Man page
hmm878 Man page
inflammFilter Man page
initialize Man page
initialize,CisConfig-method Man page
keepMapCache Man page
keepMapCache<- Man page
keepMapCache<-,CisConfig,logical-method Man page
keepMapCache,CisConfig-method Man page
lgeu Man page
locusNames Man page
mcwAllCis-class Man page
mcwBestCis-class Man page
meqtlTests Man page
meta.All.cis.eQTLs Man page
meta.best.cis.eQTLs Man page
meta.bindmaf Man page
meta.richNull Man page
meta.transScores Man page
mtransScores Man page
nperm Man page
nperm<- Man page
nperm<-,CisConfig,integer-method Man page
nperm,CisConfig-method Man page
nthScores Man page
pifdr Man page
plot,gwSnpScreenResult,character-method Man page
plotsens Man page
probesManaged Man page
qqhex Man page
radius Man page
radius<- Man page
radius<-,CisConfig,integer-method Man page
radius,CisConfig-method Man page
rhs Man page
rhs<- Man page
rhs<-,CisConfig,formula-method Man page
rhs<-,CisConfig,function-method Man page
rhs,CisConfig-method Man page
richNull Man page
sampsInVCF Man page
schrpref Man page
schrpref<- Man page
schrpref<-,CisConfig,character-method Man page
schrpref,CisConfig-method Man page
scoresCis Man page
sensanal Man page
sensanal,sensiCisInput,numeric-method Man page
sensiCisInput-class Man page
sensiCisOutput-class Man page
shortfac Man page
shortfac<- Man page
shortfac<-,CisConfig,integer-method Man page
shortfac,CisConfig-method Man page
show Man page
show,allCigCis-method Man page
show,allSigCis-method Man page
show,ApprRes-method Man page
show,CisConfig-method Man page
show,cisMap-method Man page
show,cwBestCis-method Man page
show,EqAppr-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,TransConfig-method Man page
show,transManager-method Man page
simpleTiling Man page
smchrpref Man page
smchrpref<- Man page
smchrpref<-,CisConfig,character-method Man page
smchrpref,CisConfig-method Man page
smFilter Man page
smFilter<- Man page
smFilter<-,CisConfig,function-method Man page
smFilter,CisConfig-method Man page
smpack Man page
smpack<- Man page
smpack<-,CisConfig,character-method Man page
smpack,CisConfig-method Man page
snpannopk Man page
snpannopk<- Man page
snpannopk<-,CisConfig,character-method Man page
snpannopk,CisConfig-method Man page
snpchr Man page
snpchr<- Man page
snpchr<-,TransConfig,character-method Man page
snpchr,TransConfig-method Man page
snplocsDefault Man page
snpsManaged Man page
SSgen Man page
SSgen<- Man page
SSgen<-,CisConfig,function-method Man page
SSgen,CisConfig-method Man page
strMultPop Man page
TabixFile Man page
topFeats Man page
topFeats,probeId,eqtlTestsManager-method Man page
topFeats,rsid,eqtlTestsManager-method Man page
topGenes Man page
topScores Man page
topSnps Man page
topSnps,gwSnpScreenResult-method Man page
tr1_obs Man page
tr1_perm Man page
TransConfig-class Man page
transeqByChrom Man page
transeqByCluster 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
update_fdr_filt Man page
vcf2sm Man page
vcf2sm,TabixFile,GRanges,integer-method Man page

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

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