cpvSNP

Package: cpvSNP
Type: Package
Title: Gene set analysis methods for SNP association p-values that lie
in genes in given gene sets
Version: 1.4.0
Date: 2015-04-09
Author: Caitlin McHugh, Jessica Larson, and Jason Hackney
Maintainer: Caitlin McHugh <mchughc@uw.edu>
Imports: methods, corpcor, BiocParallel, ggplot2, plyr
Depends: R (>= 2.10), GenomicFeatures, GSEABase (>= 1.24.0)
Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics,
ReportingTools, BiocStyle
Description: Gene set analysis methods exist to combine SNP-level
association p-values into gene sets, calculating a single
association p-value for each gene set. This package implements
two such methods that require only the calculated SNP p-values,
the gene set(s) of interest, and a correlation matrix (if
desired). One method (GLOSSI) requires independent SNPs and the
other (VEGAS) can take into account correlation (LD) among the
SNPs. Built-in plotting functions are available to help users
visualize results.
License: Artistic-2.0
biocViews: Genetics, StatisticalMethod, Pathways, GeneSetEnrichment,
GenomicVariation
NeedsCompilation: no
Packaged: 2016-05-04 05:57:21 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'cpvSNP' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'cpvSNP'
    finding HTML links ... done
    GLOSSIResult-class                      html  
    GLOSSIResultCollection-class            html  
    GeneSetResult-class                     html  
    GeneSetResultCollection-class           html  
    VEGASResult-class                       html  
    VEGASResultCollection-class             html  
    assocPvalBySetPlot                      html  
    createArrayData                         html  
    degreesOfFreedom-method                 html  
    exampleArrayData                        html  
    geneSetAnalysis                         html  
    geneSetName-methods                     html  
    geneSets                                html  
    geneToSNPList                           html  
    glossi                                  html  
    glossiMarginal                          html  
    pValue-method                           html  
    plotPvals                               html  
    show-methods                            html  
    simulate_chisq                          html  
    simulatedStats-method                   html  
    statistic-methods                       html  
    vegas                                   html  
    vegasMarginal                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cpvSNP)
Making 'packages.html' ... done