metaCCA: Summary Statistics-Based Multivariate Meta-Analysis of Genome-Wide Association Studies Using Canonical Correlation Analysis

metaCCA performs multivariate analysis of a single or multiple GWAS based on univariate regression coefficients. It allows multivariate representation of both phenotype and genotype. metaCCA extends the statistical technique of canonical correlation analysis to the setting where original individual-level records are not available, and employs a covariance shrinkage algorithm to achieve robustness.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("metaCCA")
AuthorAnna Cichonska <anna.cichonska@helsinki.fi>
Bioconductor views Genetics GenomeWideAssociation Regression SNP Software StatisticalMethod
Date of publicationNone
MaintainerAnna Cichonska <anna.cichonska@helsinki.fi>
LicenseMIT + file LICENSE
Version1.2.0
http://biorxiv.org/content/early/2015/07/16/022665

View on Bioconductor

Files

DESCRIPTION
LICENSE
NAMESPACE
R
R/estimateSyy.R R/expM.R R/metaCcaGp.R R/metaCcaPlusGp.R R/myCCA.R R/normalizeSxy.R R/optimalThreshold.R R/poolCov.R R/shrinkPSD.R R/shrinkPlus.R R/valAlleles.R
build
build/vignette.rds
data
data/testDataMetaCCA.rda
inst
inst/CITATION
inst/doc
inst/doc/metaCCA.R
inst/doc/metaCCA.Rnw
inst/doc/metaCCA.pdf
inst/extdata
inst/extdata/S_XX_study1.txt
inst/extdata/S_XX_study2.txt
inst/extdata/S_XY_full_study1.txt
inst/extdata/S_XY_full_study2.txt
inst/extdata/S_XY_study1.txt
inst/extdata/S_XY_study2.txt
man
man/N1.Rd man/N2.Rd man/S_XX_study1.Rd man/S_XX_study2.Rd man/S_XY_full_study1.Rd man/S_XY_full_study2.Rd man/S_XY_study1.Rd man/S_XY_study2.Rd man/estimateSyy.Rd man/metaCcaGp.Rd man/metaCcaPlusGp.Rd
vignettes
vignettes/metaCCA-concordance.tex
vignettes/metaCCA.Rnw

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