kimod: A k-tables approach to integrate multiple Omics-Data
Version 1.4.0

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
Bioconductor views ExperimentData GeneExpression Microarray Proteomics Visualization
Date of publicationNone
MaintainerM L Zingaretti <m.lau.zingaretti@gmail.com>
LicenseGPL (>=2)
Version1.4.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("kimod")

Popular man pages

Bootstrap-print.Boot: 'print' or 'summary' 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-RVPlot: Plot a 'RVPlot' of a DiStatis object
DiStatis-TrajPlot: Plot a 'TrajPlot' of a DiStatis object
GroupProj-Class: Class 'GroupProj' GroupProj S4 class (kimod: k-tables...
See all...

All man pages Function index File listing

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.

Functions

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/Auxiliares.R
R/Bootstrap-BootPlot.R
R/Bootstrap-Class.R
R/Bootstrap-print.R
R/CalculateDist.R
R/ComputeDistances.R
R/DiStatis-Bootstrap.R
R/DiStatis-Class.R
R/DiStatis-CompPlot.R
R/DiStatis-DiStatis.R
R/DiStatis-PanelPlot.R
R/DiStatis-RVPlot.R
R/DiStatis-SelectVar.R
R/DiStatis-TrajPlot.R
R/DiStatis-print.R
R/GroupProj-Class.R
R/GroupProj-print.R
R/GroupProj.R
R/ReadData.R
R/SelectVar-Biplot.R
R/SelectVar-Class.R
R/SelectVar-print.R
R/cbinPad.R
build
build/vignette.rds
data
data/NCI60Selec.RData
data/NCI60Selec_ESet.RData
data/winesassesors.RData
inst
inst/doc
inst/doc/kimod-vignette.R
inst/doc/kimod-vignette.Rnw
inst/doc/kimod-vignette.pdf
man
man/BootPlot.Rd
man/Bootstrap-Class.Rd
man/Bootstrap-print.Boot.Rd
man/Bootstrap-summary.Rd
man/DiStatis-Bootstrap.Rd
man/DiStatis-Class.Rd
man/DiStatis-CompPlot.Rd
man/DiStatis-DiStatis.Rd
man/DiStatis-PanelPlot.Rd
man/DiStatis-RVPlot.Rd
man/DiStatis-SelectVar.Rd
man/DiStatis-TrajPlot.Rd
man/DiStatis-print.Rd
man/DiStatis-summary.Rd
man/GroupProj-Class.Rd
man/GroupProj-print.Rd
man/GroupProj-summary.Rd
man/GroupProj.Rd
man/NCI60Selec.Rd
man/NCI60Selec_ESet.Rd
man/SelectVar-Biplot.Rd
man/SelectVar-Class.Rd
man/SelectVar-print.Rd
man/SelectVar-summary.Rd
man/winesassesors.Rd
vignettes
vignettes/authblk.sty
vignettes/cites.bib
vignettes/kimod-vignette.Rnw
kimod documentation built on May 20, 2017, 9:18 p.m.

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

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.