kimod: A k-tables approach to integrate multiple Omics-Data

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.

Author
Maria Laura Zingaretti, Johanna Altair Demey-Zambrano, Jose Luis Vicente-Villardon, Jhonny Rafael Demey
Date of publication
None
Maintainer
M L Zingaretti <m.lau.zingaretti@gmail.com>
License
GPL (>=2)
Version
1.2.0

View on Bioconductor

Man pages

BootPlot
Plot a 'BootPlot' of a Bootstrap object
Bootstrap-Class
Class 'Bootstrap': Bootstrap S4 class (kimod: k-tables...
Bootstrap-print.Boot
'print' or 'summary' a Bootstrap object
Bootstrap-summary
'print.Bootstrap' or 'summary.Bootstrap' a Bootstrap object
DiStatis-Bootstrap
Funtion 'Bootstrap' of a DiStatis object
DiStatis-Class
Class 'DiStatis' DiStatis S4 class (kimod: k-tables approach...
DiStatis-CompPlot
Plot a 'CompPlot' of a DiStatis object
DiStatis-DiStatis
'DiStatis' of a DiStatis object High level constructor of...
DiStatis-PanelPlot
Plot a 'PanelPlot' of a DiStatis object
DiStatis-print
'print.DiStatis' a DiStatis object Generic Print/Summary...
DiStatis-RVPlot
Plot a 'RVPlot' of a DiStatis object
DiStatis-SelectVar
Function 'SelectVar' of DiStatis object
DiStatis-summary
'summary.DiStatis' a DiStatis object
DiStatis-TrajPlot
Plot a 'TrajPlot' of a DiStatis object
GroupProj
'GroupProj' of SelectVar object
GroupProj-Class
Class 'GroupProj' GroupProj S4 class (kimod: k-tables...
GroupProj-print
'print.GP' a GroupProj object Generic print.GP method for...
GroupProj-summary
'summary.GP' a GroupProj object
NCI60Selec
Microarray gene expression profiles of the NCI 60 cell lines...
NCI60Selec_ESet
Microarray gene expression profiles of the NCI 60 cell lines...
SelectVar-Biplot
Plot a 'Biplot' of a SelectVar class object
SelectVar-Class
Class 'SelectVar' S4 class (kimod: k-tables approach to...
SelectVar-print
'print.SV' a SelectVar object Generic Print/Summary method...
SelectVar-summary
'summary' a SelectVar object Generic Print/Summary method for...
winesassesors
Description of a set of wines by a group of expert assessors.

Files in this package

kimod/DESCRIPTION
kimod/NAMESPACE
kimod/NEWS
kimod/R
kimod/R/Auxiliares.R
kimod/R/Bootstrap-BootPlot.R
kimod/R/Bootstrap-Class.R
kimod/R/Bootstrap-print.R
kimod/R/CalculateDist.R
kimod/R/ComputeDistances.R
kimod/R/DiStatis-Bootstrap.R
kimod/R/DiStatis-Class.R
kimod/R/DiStatis-CompPlot.R
kimod/R/DiStatis-DiStatis.R
kimod/R/DiStatis-PanelPlot.R
kimod/R/DiStatis-RVPlot.R
kimod/R/DiStatis-SelectVar.R
kimod/R/DiStatis-TrajPlot.R
kimod/R/DiStatis-print.R
kimod/R/GroupProj-Class.R
kimod/R/GroupProj-print.R
kimod/R/GroupProj.R
kimod/R/ReadData.R
kimod/R/SelectVar-Biplot.R
kimod/R/SelectVar-Class.R
kimod/R/SelectVar-print.R
kimod/R/cbinPad.R
kimod/build
kimod/build/vignette.rds
kimod/data
kimod/data/NCI60Selec.RData
kimod/data/NCI60Selec_ESet.RData
kimod/data/winesassesors.RData
kimod/inst
kimod/inst/doc
kimod/inst/doc/kimod-vignette.R
kimod/inst/doc/kimod-vignette.Rnw
kimod/inst/doc/kimod-vignette.pdf
kimod/man
kimod/man/BootPlot.Rd
kimod/man/Bootstrap-Class.Rd
kimod/man/Bootstrap-print.Boot.Rd
kimod/man/Bootstrap-summary.Rd
kimod/man/DiStatis-Bootstrap.Rd
kimod/man/DiStatis-Class.Rd
kimod/man/DiStatis-CompPlot.Rd
kimod/man/DiStatis-DiStatis.Rd
kimod/man/DiStatis-PanelPlot.Rd
kimod/man/DiStatis-RVPlot.Rd
kimod/man/DiStatis-SelectVar.Rd
kimod/man/DiStatis-TrajPlot.Rd
kimod/man/DiStatis-print.Rd
kimod/man/DiStatis-summary.Rd
kimod/man/GroupProj-Class.Rd
kimod/man/GroupProj-print.Rd
kimod/man/GroupProj-summary.Rd
kimod/man/GroupProj.Rd
kimod/man/NCI60Selec.Rd
kimod/man/NCI60Selec_ESet.Rd
kimod/man/SelectVar-Biplot.Rd
kimod/man/SelectVar-Class.Rd
kimod/man/SelectVar-print.Rd
kimod/man/SelectVar-summary.Rd
kimod/man/winesassesors.Rd
kimod/vignettes
kimod/vignettes/authblk.sty
kimod/vignettes/cites.bib
kimod/vignettes/kimod-vignette.Rnw