gQTLstats: gQTLstats: computationally efficient analysis for eQTL and allied studies

computationally efficient analysis of eQTL, mQTL, dsQTL, etc.

Author
VJ Carey <stvjc@channing.harvard.edu>
Date of publication
None
Maintainer
VJ Carey <stvjc@channing.harvard.edu>
License
Artistic-2.0
Version
1.6.0

View on Bioconductor

Man pages

cisAssoc
test for variant-expression associations in cis, using VCF
clipPCs
transformations of expression data in smlSet instances
directPlot
visualize relationship between empirical and modeled FDR...
enumerateByFDR
filter a ciseStore instance using an FDR threshold
eqBox2
visualization of expression or other assay measure against...
FDRsupp-class
Class '"FDRsupp"'
filtFDR
illustration of FDRsupp class
gQTLs
use SummarizedExperiment to manage a collection of gQTL...
gQTLstats-package
\Sexpr[results=rd,stage=build]{tools:::Rd_package_title("gQTLstats")}
hmm878
labeled GRanges with ChromHMM chromatin states for GM12878
manhWngr
manhattan plot with named GRanges
mixedVCFtoSnpMatrix
amalgamate called genotypes and imputed allelic dosages in...
pifdr
utility for computing plug-in FDR
qqStore
create a binned QQplot for a sharded store
queryVCF
obtain SnpMatrix from VCF genotypes
senstab
create a plottable table for eQTL sensitivity analysis...
setFDRfunc
estimate and store function relating association scores to...
storeToStats
extract a vector from store results as ff (out of memory...
transAssoc
compute 'trans' SNP-feature associations by wrapping AllAssoc
TransStore
Instance constructor for managing trans gQTL results
TransStore-class
Class '"TransStore"'
txsPlot
visualize transformed FDR against transformed association...

Files in this package

gQTLstats/DESCRIPTION
gQTLstats/NAMESPACE
gQTLstats/R
gQTLstats/R/allS4.R
gQTLstats/R/buf.R
gQTLstats/R/bufferedTrans.R
gQTLstats/R/cisAssocPlus.R
gQTLstats/R/cisCount.R
gQTLstats/R/cisEsts.R
gQTLstats/R/filters.R
gQTLstats/R/gmod2.R
gQTLstats/R/manhW878.R
gQTLstats/R/mixedVcfToSM.R
gQTLstats/R/pifdr.R
gQTLstats/R/plot.sensobj.thresh.R
gQTLstats/R/qqStore.R
gQTLstats/R/queryVCF.R
gQTLstats/R/senstab.R
gQTLstats/R/storeStats.R
gQTLstats/R/transChunk.R
gQTLstats/build
gQTLstats/build/partial.rdb
gQTLstats/build/vignette.rds
gQTLstats/data
gQTLstats/data/bigfiltFDR.rda
gQTLstats/data/bigrawFDR.rda
gQTLstats/data/datalist
gQTLstats/data/filtFDR.rda
gQTLstats/data/hmm878.rda
gQTLstats/data/rawFDR.rda
gQTLstats/data/sensByProbe.rda
gQTLstats/data/sigInlit.rda
gQTLstats/inst
gQTLstats/inst/doc
gQTLstats/inst/doc/gQTLstats.R
gQTLstats/inst/doc/gQTLstats.Rmd
gQTLstats/inst/doc/gQTLstats.html
gQTLstats/inst/scripts
gQTLstats/inst/scripts/README.txt
gQTLstats/inst/scripts/geuvFull
gQTLstats/inst/scripts/geuvFull/gsvs.rda
gQTLstats/inst/scripts/geuvFull/runit.R
gQTLstats/inst/scripts/geuvFull/runit3.R
gQTLstats/inst/scripts/geuvFull/tg_250k.rda
gQTLstats/inst/scripts/sensByProbe
gQTLstats/inst/scripts/sensByProbe/sensanal2.R
gQTLstats/inst/scripts/sensBySNP
gQTLstats/inst/scripts/sensBySNP/bysnpBat.R
gQTLstats/inst/unitTests
gQTLstats/inst/unitTests/test_gQTLstats.R
gQTLstats/inst/vcf
gQTLstats/inst/vcf/GLdemo.vcf
gQTLstats/inst/vcf/README.txt
gQTLstats/inst/vcf/c20exch.vcf.gz
gQTLstats/inst/vcf/c20exch.vcf.gz.tbi
gQTLstats/inst/vcf/lit20.vcf.gz
gQTLstats/inst/vcf/lit20.vcf.gz.tbi
gQTLstats/inst/vcf/litv.vcf.gz
gQTLstats/inst/vcf/litv.vcf.gz.tbi
gQTLstats/inst/vcf/mixedVcfToSM.R
gQTLstats/inst/vcf/polytype.vcf
gQTLstats/inst/vcf/polytypeSNV.vcf
gQTLstats/inst/vcf/small_1.vcf.gz
gQTLstats/inst/vcf/small_1.vcf.gz.tbi
gQTLstats/man
gQTLstats/man/FDRsupp-class.Rd
gQTLstats/man/TransStore-class.Rd
gQTLstats/man/TransStore.Rd
gQTLstats/man/cisAssoc.Rd
gQTLstats/man/clipPCs.Rd
gQTLstats/man/directPlot.Rd
gQTLstats/man/enumerateByFDR.Rd
gQTLstats/man/eqBox2.Rd
gQTLstats/man/filtFDR.Rd
gQTLstats/man/gQTLs.Rd
gQTLstats/man/gQTLstats-package.Rd
gQTLstats/man/hmm878.Rd
gQTLstats/man/manhWngr.Rd
gQTLstats/man/mixedVCFtoSnpMatrix.Rd
gQTLstats/man/pifdr.Rd
gQTLstats/man/qqStore.Rd
gQTLstats/man/queryVCF.Rd
gQTLstats/man/senstab.Rd
gQTLstats/man/setFDRfunc.Rd
gQTLstats/man/storeToStats.Rd
gQTLstats/man/transAssoc.Rd
gQTLstats/man/txsPlot.Rd
gQTLstats/tests
gQTLstats/tests/test-all.R
gQTLstats/vignettes
gQTLstats/vignettes/gQTLstats.Rmd