coloc: Colocalisation tests of two genetic traits

Performs the colocalisation tests described in Plagnol et al (2009), Wallace et al (2013) and Giambartolomei et al (2013).

Author
Chris Wallace [aut, cre], Claudia Giambartolomei [aut], Vincent Plagnol [ctb]
Date of publication
2013-09-29 17:23:08
Maintainer
Chris Wallace <chris.wallace@cimr.cam.ac.uk>
License
GPL
Version
2.3-1
URLs

View on CRAN

Man pages

approx.bf.estimates
Internal function, approx.bf.estimates
approx.bf.p
Internal function, approx.bf.p
bf
Bayes factors to compare specific values of eta
coloc.abf
Fully Bayesian colocalisation analysis using Bayes Factors
coloc.abf.datasets
Bayesian colocalisation analysis using data.frames
coloc.abf.snpStats
Bayesian colocalisation analysis using snpStats objects
coloc.bma
Wrapper to use colocalization testing within a Bayesian model...
coloc-class
Classes '"coloc"' and '"colocBayes"'
coloc-package
Colocalisation tests of two genetic traits
colocPCs-class
Class '"colocPCs"'
coloc.test
Function to do colocalisation tests of two traits
coloc.test.summary
Colocalisation testing using regression coefficients
combine.abf
combine.abf
eta
Methods to extract information from a 'coloc' or 'colocBayes'...
fillin
Impute missing genotypes
logdiff
logdiff
logsum
logsum
pcs.model
pcs.model
pcs.prepare
Functions to prepare principle component models for...
process.dataset
process.dataset
sdY.est
Estimate trait variance, internal function
Var.data
Var.data
Var.data.cc
Var.data

Files in this package

coloc
coloc/inst
coloc/inst/CITATION
coloc/inst/tests
coloc/inst/tests/test.txt
coloc/inst/tests/test-abf.R
coloc/inst/doc
coloc/inst/doc/vignette.Rnw
coloc/inst/doc/vignette.pdf
coloc/inst/doc/vignette.R
coloc/NAMESPACE
coloc/R
coloc/R/AllClasses.R
coloc/R/pcs.R
coloc/R/bma.R
coloc/R/coloc.test.R
coloc/R/claudia.R
coloc/R/coloc.combine.R
coloc/R/private.R
coloc/R/coloc-package.R
coloc/vignettes
coloc/vignettes/vignette.Rnw
coloc/vignettes/vignette.org
coloc/MD5
coloc/build
coloc/build/vignette.rds
coloc/DESCRIPTION
coloc/ChangeLog
coloc/man
coloc/man/coloc.test.summary.Rd
coloc/man/coloc.abf.snpStats.Rd
coloc/man/logdiff.Rd
coloc/man/coloc.abf.Rd
coloc/man/approx.bf.p.Rd
coloc/man/coloc-package.Rd
coloc/man/coloc-class.Rd
coloc/man/sdY.est.Rd
coloc/man/Var.data.cc.Rd
coloc/man/Var.data.Rd
coloc/man/fillin.Rd
coloc/man/combine.abf.Rd
coloc/man/approx.bf.estimates.Rd
coloc/man/pcs.prepare.Rd
coloc/man/coloc.test.Rd
coloc/man/coloc.bma.Rd
coloc/man/eta.Rd
coloc/man/coloc.abf.datasets.Rd
coloc/man/pcs.model.Rd
coloc/man/process.dataset.Rd
coloc/man/colocPCs-class.Rd
coloc/man/bf.Rd
coloc/man/logsum.Rd