kimod

Package: kimod
Type: Package
Title: A k-tables approach to integrate multiple Omics-Data
Version: 1.0.0
Date: 2015-12-7
Author: Maria Laura Zingaretti, Johanna Altair Demey-Zambrano, Jose Luis Vicente-Villardon, Jhonny Rafael Demey
Maintainer: M L Zingaretti <m.lau.zingaretti@gmail.com>
Description: This package allows to work with mixed omics data (transcriptomics, proteomics, microarray-chips, rna-seq data), introducing the following
improvements: distance options (for numeric and/or categorical variables) for each of the tables, bootstrap resampling techniques on the
residuals matrices for all methods, that enable perform confidence ellipses for the projection of individuals, variables and biplot
methodology to project variables (gene expression) on the compromise. Since the main purpose of the package is to use these techniques to
omic data analysis, it includes an example data from four different microarray platforms (i.e.,Agilent, Affymetrix HGU 95, Affymetrix HGU
133 and Affymetrix HGU 133plus 2.0) on the NCI-60 cell lines.NCI60_4arrays is a list containing the NCI-60 microarray data with only few
hundreds of genes randomly selected in each platform to keep the size of the package small. The data are the same that the package omicade4
used to implement the co-inertia analysis. The references in packages follow the style of the APA-6th norm.
License: GPL (>=2)
LazyData: TRUE
biocViews: Microarray, Visualization, GeneExpression, ExperimentData,
Proteomics
Depends: R (>= 3.3), methods
Imports: cluster, graphics, Biobase
Collate: 'ReadData.R' 'DiStatis-Class.R' 'Bootstrap-Class.R'
'SelectVar-Class.R' 'GroupProj-Class.R' 'Auxiliares.R'
'CalculateDist.R' 'ComputeDistances.R' 'cbinPad.R'
'DiStatis-DiStatis.R' 'DiStatis-CompPlot.R' 'DiStatis-RVPlot.R'
'DiStatis-PanelPlot.R' 'DiStatis-TrajPlot.R' 'DiStatis-print.R'
'DiStatis-Bootstrap.R' 'Bootstrap-BootPlot.R'
'Bootstrap-print.R' 'DiStatis-SelectVar.R' 'SelectVar-print.R'
'SelectVar-Biplot.R' 'GroupProj.R' 'GroupProj-print.R'
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-04 06:42:32 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'kimod' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for 'print' from package 'base' in package 'kimod'
Creating a generic function for 'summary' from package 'base' in package 'kimod'
** help
*** installing help indices
  converting help for package 'kimod'
    finding HTML links ... done
    BootPlot                                html  
    Bootstrap-Class                         html  
    Bootstrap-print.Boot                    html  
    Bootstrap-summary                       html  
    DiStatis-Bootstrap                      html  
    DiStatis-Class                          html  
    DiStatis-CompPlot                       html  
    DiStatis-DiStatis                       html  
    DiStatis-PanelPlot                      html  
    DiStatis-RVPlot                         html  
    DiStatis-SelectVar                      html  
    DiStatis-TrajPlot                       html  
    DiStatis-print                          html  
    DiStatis-summary                        html  
    GroupProj-Class                         html  
    GroupProj-print                         html  
    GroupProj-summary                       html  
    GroupProj                               html  
    NCI60Selec                              html  
    NCI60Selec_ESet                         html  
    SelectVar-Biplot                        html  
    SelectVar-Class                         html  
    SelectVar-print                         html  
    SelectVar-summary                       html  
    winesassesors                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (kimod)
Making 'packages.html' ... done