metaCCA: Summary Statistics-Based Multivariate Meta-Analysis of Genome-Wide Association Studies Using Canonical Correlation Analysis
Version 1.4.0

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.

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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
Version1.4.0
URL http://biorxiv.org/content/early/2015/07/16/022665
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("metaCCA")

Man pages

estimateSyy: Function to estimate correlations between phenotypic...
metaCcaGp: Function to perform genotype-phenotype association analysis...
metaCcaPlusGp: Function to perform genotype-phenotype association analysis...
N1: Number of individuals in study 1.
N2: Number of individuals in study 2.
S_XX_study1: Correlations between 10 SNPs corresponding to the population...
S_XX_study2: Correlations between 10 SNPs corresponding to the population...
S_XY_full_study1: Univariate summary statistics of 10 traits across 1000 SNPs...
S_XY_full_study2: Univariate summary statistics of 10 traits across 1000 SNPs...
S_XY_study1: Univariate summary statistics of 10 traits across 10 SNPs...
S_XY_study2: Univariate summary statistics of 10 traits across 10 SNPs...

Functions

N1 Man page
N2 Man page
S_XX_study1 Man page
S_XX_study2 Man page
S_XY_full_study1 Man page
S_XY_full_study2 Man page
S_XY_study1 Man page
S_XY_study2 Man page
estimateSyy Man page Source code
expM Source code
metaCcaGp Man page Source code
metaCcaPlusGp Man page Source code
myCCA Source code
normalizeSxy Source code
optimalThreshold Source code
poolCov Source code
shrinkPSD Source code
shrinkPlus Source code
valAlleles Source code

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.Rnw
metaCCA documentation built on May 20, 2017, 9:24 p.m.