MultiMeta

Package: MultiMeta
Type: Package
Title: Meta-analysis of Multivariate Genome Wide Association Studies
Version: 0.1
Date: 2014-08-21
Author: Dragana Vuckovic
Maintainer: Dragana Vuckovic <dragana.vuckovic@burlo.trieste.it>
Description: 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.
License: GPL (>= 2)
Imports: mvtnorm, expm, ggplot2, reshape2
Depends: gtable, grid
Collate: 'betas_plot.R' 'mhplot.R' 'multi_meta.R' 'qqplotter.R'
'Example_file_1.R' 'Example_file_2.R' 'Example_output_file.R'
Packaged: 2015-01-15 08:57:26 UTC; genetica
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2015-01-15 11:44:10

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'MultiMeta' ...
** package 'MultiMeta' successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'MultiMeta'
    finding HTML links ... done
    Example_file_1                          html  
    Example_file_2                          html  
    Example_output_file                     html  
    betas_plot                              html  
    mhplot                                  html  
    multi_meta                              html  
    qqplotter                               html  
** building package indices
** testing if installed package can be loaded
* DONE (MultiMeta)
Making 'packages.html' ... done