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.

AuthorMaria Laura Zingaretti, Johanna Altair Demey-Zambrano, Jose Luis Vicente-Villardon, Jhonny Rafael Demey
Date of publicationNone
MaintainerM L Zingaretti <m.lau.zingaretti@gmail.com>
LicenseGPL (>=2)
Version1.2.0

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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