mGSZ

Package: mGSZ
Type: Package
Title: Gene set analysis based on GSZ-scoring function and asymptotic
p-value
Version: 1.0
Date: 2014-02-19
Author: Pashupati Mishra, Petri Toronen
Maintainer: Pashupati Mishra <pashupati.mishra@helsinki.fi>
Depends: R (>= 3.0.0), Biobase, GSA, limma, MASS, ismev
Description: Performs gene set analysis based on GSZ scoring function and asymptotic p-value. It is different from GSZ in that it implements asymptotic p-values instead of empirical p-values. Asymptotic p-values are calculated by fitting suitable distribution model to the null distribution. Unlike empirical p-values, resolution of asymptotic p-values are independent of the number of permutations and hence requires considerably fewer permutations. In addition, this package allows gene set analysis with seven other popular gene set analysis methods.
License: GPL (>= 2)
Packaged: 2014-02-19 10:16:18 UTC; pashu
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-02-19 12:24:13

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'mGSZ' ...
** package 'mGSZ' successfully unpacked and MD5 sums checked
** R
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'mGSZ'
    finding HTML links ... done
    FC_int                                  html  
    KS.p.values_int                         html  
    KS.score_int                            html  
    SS.p.values_int                         html  
    SS.test.score_int                       html  
    StabPlotData                            html  
    WRS.p.values_int                        html  
    WRS.test.score_int                      html  
    calc.z.var_int                          html  
    count.hyge.var.mean_int                 html  
    count.prob.sum_int                      html  
    diffFCscore_int                         html  
    diffScore_int                           html  
    emp.wrs_int                             html  
    emp_int                                 html  
    flipListStruct_int                      html  
    geneSetsList                            html  
    listTOclMatrix_int                      html  
    logEVcdf_int                            html  
    logNORMcdf_int                          html  
    mAllez.p.values_int                     html  
    mGSA.p.values_int                       html  
    mGSZ                                    html  
    mGSZ.adj.mean.std_int                   html  
    mGSZ.p.values_int                       html  
    mGSZ.test.score.stb2_int                html  
    mGSZ.test.score.stb3_int                html  
    mGSZ.test.score.stb4_int                html  
    mGSZ.test.score2_int                    html  
    mGSZ.test.score4_int                    html  
    mGSZ.test.score_int                     html  
    pick.data.cols_int                      html  
    plotProfile                             html  
    rm.rows.with.noSetMembers_int           html  
    rm.small.genesets_int                   html  
    sumTestscore_int                        html  
    sumVarMean.calc_int                     html  
    toMatrix_int                            html  
    toTable                                 html  
** building package indices
** testing if installed package can be loaded
* DONE (mGSZ)
Making 'packages.html' ... done