MultiMeta: Meta-analysis of Multivariate Genome Wide Association Studies

Allows running a meta-analysis of multivariate Genome Wide Association Studies (GWAS) and easily visualizing results through custom plotting functions. The multivariate setting implies that results for each single nucleotide polymorphism (SNP) include several effect sizes (also known as "beta coefficients", one for each trait), as well as related variance values, but also covariance between the betas. The main goal of the package is to provide combined beta coefficients across different cohorts, together with the combined variance/covariance matrix. The method is inverse-variance based, thus each beta is weighted by the inverse of its variance-covariance matrix, before taking the average across all betas. The default options of the main function \code{multi_meta} will work with files obtained from GEMMA multivariate option for GWAS (Zhou & Stephens, 2014). It will work with any other output, as soon as columns are formatted to have the according names. The package also provides several plotting functions for QQ-plots, Manhattan Plots and custom summary plots.

Author
Dragana Vuckovic
Date of publication
2015-01-15 11:44:10
Maintainer
Dragana Vuckovic <dragana.vuckovic@burlo.trieste.it>
License
GPL (>= 2)
Version
0.1

View on CRAN

Man pages

betas_plot
Summary plot of the effect sizes and their correlations for a...
Example_file_1
Example data file 1
Example_file_2
Example data file 2
Example_output_file
Example output file
mhplot
Manhattan Plot for meta-analysis results
multi_meta
Meta-analysis of multivariate GWAS results
qqplotter
Quantile-quantile plot for observed vs. expected p-values

Files in this package

MultiMeta
MultiMeta/inst
MultiMeta/inst/extdata
MultiMeta/inst/extdata/Example_file_1.txt
MultiMeta/inst/extdata/Example_output_file.txt
MultiMeta/inst/extdata/Example_file_2.txt
MultiMeta/NAMESPACE
MultiMeta/R
MultiMeta/R/Example_file_2.R
MultiMeta/R/betas_plot.R
MultiMeta/R/Example_file_1.R
MultiMeta/R/multi_meta.R
MultiMeta/R/mhplot.R
MultiMeta/R/qqplotter.R
MultiMeta/R/Example_output_file.R
MultiMeta/MD5
MultiMeta/DESCRIPTION
MultiMeta/man
MultiMeta/man/Example_file_2.Rd
MultiMeta/man/mhplot.Rd
MultiMeta/man/betas_plot.Rd
MultiMeta/man/Example_output_file.Rd
MultiMeta/man/Example_file_1.Rd
MultiMeta/man/qqplotter.Rd
MultiMeta/man/multi_meta.Rd