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

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

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

View on Bioconductor

Man pages

cisAssoc: test for variant-expression associations in cis or generally,...

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: gQTLstats: computationally efficient analysis for eQTL and...

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...

tqbrowser: general browsing facility for trans-gQTL

transAssoc: compute 'trans' SNP-feature associations by wrapping AllAssoc

transBrowse: shiny app to exhibit genotype:genomic feature distributions

TransStore: Instance constructor for managing trans gQTL results

TransStore-class: Class '"TransStore"'

tsByRank: harvest contents of a TransStore by rank in associations of...

txsPlot: visualize transformed FDR against transformed association...

Functions

AllAssoc Man page
cisAssoc Man page
cisCount Man page
cisEsts Man page
clipPCs Man page
clipPCs,RangedSummarizedExperiment,numeric,logical-method Man page
clipPCs,RangedSummarizedExperiment,numeric,missing-method Man page
clipPCs,SummarizedExperiment,numeric,logical-method Man page
clipPCs,SummarizedExperiment,numeric,missing-method Man page
collapse_multiPerm Man page
describe Man page
describe,TransStore-method Man page
directPlot Man page
distToGene Man page
enumerateByFDR Man page
eqBox2 Man page
eqBox3 Man page
eqDesc2 Man page
FDRsupp-class Man page
filteredDFwPerm Man page
filtFDR Man page
getFDRfunc Man page
getFDRfunc,FDRsupp-method Man page
getTab Man page
getTab,FDRsupp-method Man page
getTransRegistries Man page
gQTLs Man page
gQTLstats Man page
gQTLstats-package Man page
gQTLswarm Man page
hmm878 Man page
manhWngr Man page
mixedVCFtoSnpMatrix Man page
pifdr Man page
pifdr2 Man page
pifdr3 Man page
plot Man page
plot.senstab Man page
prep.cisAssocNB Man page
qqStore Man page
queryVCF Man page
rawFDR Man page
regressOut Man page
sensByProbe Man page
senstab Man page
setFDRfunc Man page
storeToFDR Man page
storeToFDRByProbe Man page
storeToFf Man page
storeToHist Man page
storeToMaxAssocBySNP Man page
storeToQuantiles Man page
table_sensobj_thresh Man page
tqbrowser Man page
transAssoc Man page
transBrowse Man page
transBrowse2 Man page
TransChunk Man page
TransChunk-class Man page
TransStore Man page
TransStore-class Man page
transTable Man page
tsByRank Man page
tsByRankAccum Man page
tsByRankAccum_sing Man page
tsByRank_sing Man page
tsIndex.reg Man page
txsPlot Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/allS4.R R/bhwe.R R/buf.R R/bufferedTrans.R R/cisAssocPlus.R R/cisCount.R R/cisEsts.R R/collapse_multiPerm.R R/eqBox3.R R/filters.R R/getRegs.R R/gmod2.R R/manhW878.R R/mixedVcfToSM.R R/pifdr.R R/plot.sensobj.thresh.R R/qqStore.R R/queryVCF.R R/senstab.R R/statsByRank.R R/storeStats.R R/tqbrowser.R R/transBrowse.R R/transBrowse2.R R/transChunk.R R/tsIndex.R
build
build/partial.rdb
build/vignette.rds
data
data/bigfiltFDR.rda
data/bigrawFDR.rda
data/cyto37n.rda
data/datalist
data/filtFDR.rda
data/hmm878.rda
data/rawFDR.rda
data/sensByProbe.rda
data/sigInlit.rda
data/tbgaOrmdl3.rda
inst
inst/doc
inst/doc/gQTLstats.R
inst/doc/gQTLstats.Rmd
inst/doc/gQTLstats.html
inst/registries
inst/registries/chr17-export
inst/registries/chr17-export/BatchJobs.db
inst/registries/chr17-export/conf.RData
inst/registries/chr17-export/exports
inst/registries/chr17-export/functions
inst/registries/chr17-export/functions/ae62592fc95f62f2efa7fadeacc36f19.RData
inst/registries/chr17-export/jobs
inst/registries/chr17-export/jobs/01
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inst/registries/chr17-export/jobs/01/1.R
inst/registries/chr17-export/jobs/01/1.out
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inst/registries/chr17-export/jobs/95/95.out
inst/registries/chr17-export/pending
inst/registries/chr17-export/registry.RData
inst/registries/chr17-export/resources
inst/registries/chr17-export/resources/resources_1480823330.RData
inst/registries/chr6-export
inst/registries/chr6-export/BatchJobs.db
inst/registries/chr6-export/conf.RData
inst/registries/chr6-export/exports
inst/registries/chr6-export/functions
inst/registries/chr6-export/functions/a9ee5dd80637c905e1fcebd36385a8bc.RData
inst/registries/chr6-export/jobs
inst/registries/chr6-export/jobs/01
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inst/registries/chr6-export/jobs/01/1.R
inst/registries/chr6-export/jobs/01/1.out
inst/registries/chr6-export/jobs/02
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inst/registries/chr6-export/jobs/02/2.R
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inst/registries/chr6-export/jobs/81/81.out
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inst/registries/chr6-export/jobs/90/90.out
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inst/registries/chr6-export/jobs/91/91.out
inst/registries/chr6-export/pending
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inst/registries/chr6-export/registry.RData
inst/registries/chr6-export/resources
inst/registries/chr6-export/resources/resources_1480823186.RData
inst/registries/chr6-export/resources/resources_1480943073.RData
inst/registries/chr6-export/resources/resources_1481032968.RData
inst/scripts
inst/scripts/README.txt
inst/scripts/geuvFull
inst/scripts/geuvFull/gsvs.rda
inst/scripts/geuvFull/runit.R inst/scripts/geuvFull/runit3.R
inst/scripts/geuvFull/tg_250k.rda
inst/scripts/sensByProbe
inst/scripts/sensByProbe/sensanal2.R
inst/scripts/sensBySNP
inst/scripts/sensBySNP/bysnpBat.R
inst/unitTests
inst/unitTests/test_gQTLstats.R
inst/vcf
inst/vcf/GLdemo.vcf
inst/vcf/README.txt
inst/vcf/c20exch.vcf.gz
inst/vcf/c20exch.vcf.gz.tbi
inst/vcf/lit20.vcf.gz
inst/vcf/lit20.vcf.gz.tbi
inst/vcf/litv.vcf.gz
inst/vcf/litv.vcf.gz.tbi
inst/vcf/mixedVcfToSM.R
inst/vcf/polytype.vcf
inst/vcf/polytypeSNV.vcf
inst/vcf/small_1.vcf.gz
inst/vcf/small_1.vcf.gz.tbi
man
man/FDRsupp-class.Rd man/TransStore-class.Rd man/TransStore.Rd man/cisAssoc.Rd man/clipPCs.Rd man/directPlot.Rd man/enumerateByFDR.Rd man/eqBox2.Rd man/filtFDR.Rd man/gQTLs.Rd man/gQTLstats-package.Rd man/hmm878.Rd man/manhWngr.Rd man/mixedVCFtoSnpMatrix.Rd man/pifdr.Rd man/qqStore.Rd man/queryVCF.Rd man/senstab.Rd man/setFDRfunc.Rd man/storeToStats.Rd man/tqbrowser.Rd man/transAssoc.Rd man/transBrowse.Rd man/tsByRank.Rd man/txsPlot.Rd
tests
tests/test-all.R
vignettes
vignettes/gQTLstats.Rmd

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