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.

Author
Anna Cichonska <anna.cichonska@helsinki.fi>
Date of publication
None
Maintainer
Anna Cichonska <anna.cichonska@helsinki.fi>
License
MIT + file LICENSE
Version
1.2.0
URLs

View on Bioconductor

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...

Files in this package

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