gQTLBase: gQTLBase: infrastructure for eQTL, mQTL and similar studies
Version 1.8.0

Infrastructure for eQTL, mQTL and similar studies.

AuthorVJ Carey <stvjc@channing.harvard.edu>
Bioconductor views DataImport FunctionalGenomics Genetics GenomeAnnotation SNP
Date of publicationNone
MaintainerVJ Carey <stvjc@channing.harvard.edu>
LicenseArtistic-2.0
Version1.8.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("gQTLBase")

Getting started

gQTLBase: infrastructure for storage and interrogation of eQTL, mQTL,

Popular man pages

describeStore: collect basic descriptive statistics on ciseStore instances
extractByProbes: retrieve eqtlTest results from a ciseStore instance
gqtlBase-package: gQTLBase: infrastructure for eQTL, mQTL and similar studies
mergeCIstates: merge ChromImpute chromatin states, or GWAS hit indicators,...
storeApply: apply a function over job results in a ciseStore instance
storeMapResults: use batchMapResults infrastructure to process results in a...
storeToFf: extract a vector from store results as ff (out of memory...
See all...

All man pages Function index File listing

Man pages

ciseStore-class: Class '"ciseStore"'
describeStore: collect basic descriptive statistics on ciseStore instances
extractByProbes: retrieve eqtlTest results from a ciseStore instance
gqtlBase-package: gQTLBase: infrastructure for eQTL, mQTL and similar studies
mergeCIstates: merge ChromImpute chromatin states, or GWAS hit indicators,...
storeApply: apply a function over job results in a ciseStore instance
storeMapResults: use batchMapResults infrastructure to process results in a...
storeToFf: extract a vector from store results as ff (out of memory...
ufeatByTiling: split featurenames of SummarizedExperiment according to...

Functions

DFstoreToFf Source code
balancedFeatList Man page Source code
cb2range Source code
ciseStore Man page Source code
ciseStore-class Man page
coerce_to_highest_vmode Source code
dendroReduce.bj Source code
dendroReduce.fe Source code
describeByFilts Man page Source code
describeStore Man page Source code Source code
describeStore.old Source code
describeStore.slow Source code
describeStoreToTmpReg Source code
extractByProbes Man page Source code
extractByProbes,ciseStore,character,character-method Man page
extractByProbes,ciseStore,character,missing-method Man page
extractByRanges Man page Source code
extractByRanges,ciseStore,GRanges-method Man page
extractBySymbols Man page Source code
extractBySymbols,ciseStore,character,character,character-method Man page
extractBySymbols,ciseStore,character,character,missing-method Man page
ffapp2 Source code
gQTLBase Man page
gQTLBase-package Man page
getJobIds Source code
getResult Source code
getResultIDs Source code
getResultList Source code
getStoreIDchunks Source code
gtpath1kg Source code
jobsByChrom Source code
killTempRegistry Source code
loadAndFilterResult Man page Source code
makeProbeMap Source code
makeRangeMap Source code
makeTempRegistry Source code
matprint Man page
mergeCIstates Man page Source code
mergeGWhits Man page Source code
n.uniq.snp Source code
show Man page
show,ciseStore-method Man page
show,storeDescription-method Man page
storeApply Man page Source code
storeApply2 Source code
storeDescription-class Man page
storeMapResults Man page Source code
storeToFDR Man page
storeToFDRByProbe Man page
storeToFf Man page Source code
storeToHist Man page
storeToQuantiles Man page
ufeatByTiling Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/cb2range.R
R/d.R
R/ffapp2.R
R/gtpath.R
R/mergeToLoci.R
R/storeFuncs.R
R/storeS4.R
R/ufeatByTiling.R
build
build/partial.rdb
build/vignette.rds
inst
inst/doc
inst/doc/gQTLBase.R
inst/doc/gQTLBase.Rmd
inst/doc/gQTLBase.html
inst/unitTests
inst/unitTests/test_ciseStore.R
man
man/ciseStore-class.Rd
man/describeStore.Rd
man/extractByProbes.Rd
man/gqtlBase-package.Rd
man/mergeCIstates.Rd
man/storeApply.Rd
man/storeMapResults.Rd
man/storeToFf.Rd
man/ufeatByTiling.Rd
tests
tests/test-all.R
vignettes
vignettes/gQTLBase.Rmd
gQTLBase documentation built on May 20, 2017, 9:46 p.m.