hierGWAS: Asessing statistical significance in predictive GWA studies
Version 1.6.0

Testing individual SNPs, as well as arbitrarily large groups of SNPs in GWA studies, using a joint model of all SNPs. The method controls the FWER, and provides an automatic, data-driven refinement of the SNP clusters to smaller groups or single markers.

Browse man pages Browse package API and functions Browse package files

AuthorLaura Buzdugan
Bioconductor views Clustering LinkageDisequilibrium SNP
Date of publicationNone
MaintainerLaura Buzdugan <buzdugan@stat.math.ethz.ch>
LicenseGPL-3
Version1.6.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("hierGWAS")

Man pages

cluster.snp: Hierarchical Clustering of SNP Data
compute.r2: R2 computation
hierGWAS: Asessing statistical significance in predictive GWA studies
multisplit: Variable Selection on Random Sample Splits.
simGWAS: Simulated GWAS data
test.hierarchy: Hierarchical Testing of SNPs

Functions

adj.pval Source code
cluster.snp Man page Source code
comp.cluster.pval Source code
compute.r2 Man page Source code
hierGWAS Man page
hierGWAS-package Man page
iterative.DFS Source code
lasso.select Source code
multisplit Man page Source code
return.r2 Source code
simGWAS Man page
test.hierarchy Man page Source code
test.snp Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/MEL.R
R/adj.pval.R
R/cluster.snp.R
R/comp.cluster.pval.R
R/compute.r2.R
R/iterative.DFS.R
R/lasso.select.R
R/multisplit.R
R/return.r2.R
R/test.hierarchy.R
R/test.snp.R
build
build/vignette.rds
data
data/simGWAS.rda
inst
inst/doc
inst/doc/hierGWAS.R
inst/doc/hierGWAS.Rnw
inst/doc/hierGWAS.pdf
inst/unitTests
inst/unitTests/test_cluster.snp.R
inst/unitTests/test_multisplit.R
man
man/cluster.snp.Rd
man/compute.r2.Rd
man/hierGWAS.Rd
man/multisplit.Rd
man/simGWAS.Rd
man/test.hierarchy.Rd
tests
tests/runTests.R
vignettes
vignettes/flowchart2.pdf
vignettes/hierGWAS.Rnw
hierGWAS documentation built on May 20, 2017, 10:19 p.m.