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.

Functions

Biplot Man page
Biplot,SelectVar-method Man page
BootPlot Man page
BootPlot,Bootstrap-method Man page
Bootstrap Man page
Bootstrap-class Man page
Bootstrap,DiStatis-method Man page
Bootstrap-methods Man page
class:DiStatis Man page
Comparisions.Boot Man page
Comparisions.Boot<-,Bootstrap-method Man page
Comparisions.Boot,Bootstrap-method Man page
CompPlot Man page
CompPlot,DiStatis-method Man page
Compromise.Coords Man page
Compromise.Coords<-,DiStatis-method Man page
Compromise.Coords,DiStatis-method Man page
Compromise.Matrix Man page
Compromise.Matrix<-,DiStatis-method Man page
Compromise.Matrix,DiStatis-method Man page
Coord.Select Man page
Coord.Select<-,SelectVar-method Man page
Coord.Select,SelectVar-method Man page
Coord.Select,SelectVar-method Man page
DiStatis Man page
DiStatis-class Man page
DiStatis-class Man page
DiStatis-methods Man page
EigValues.Boot Man page
EigValues.Boot<-,Bootstrap-method Man page
EigValues.Boot,Bootstrap-method Man page
Elipses.Boot Man page
Elipses.Boot<-,Bootstrap-method Man page
Elipses.Boot,Bootstrap-method Man page
Euclid.Im Man page
Euclid.Im<-,DiStatis-method Man page
Euclid.Im,DiStatis-method Man page
GroupProj Man page
GroupProj-class Man page
GroupProj,SelectVar-method Man page
GroupProj-SelectVar-methods Man page
Groups Man page
Groups<-,GroupProj-method Man page
Groups,GroupProj-method Man page
Inertia.Boot Man page
Inertia.Boot<-,Bootstrap-method Man page
Inertia.Boot,Bootstrap-method Man page
Inertia.comp Man page
Inertia.comp<-,DiStatis-method Man page
Inertia.comp,DiStatis-method Man page
Inertia.RV Man page
Inertia.RV<-,DiStatis-method Man page
Inertia.RV,DiStatis-method Man page
List.Selec.Est Man page
List.Selec.Est<-,SelectVar-method Man page
List.Selec.Est,SelectVar-method Man page
List.Selec.Var Man page
List.Selec.Var<-,SelectVar-method Man page
List.Selec.Var,SelectVar-method Man page
NCI60Selec Man page
NCI60Selec_ESet Man page
PanelPlot Man page
PanelPlot,DiStatis-method Man page
print.Bootstrap Man page
print,Bootstrap-method Man page
print.DiStatis Man page
print,DiStatis-method Man page
print.GP Man page
print,GroupProj-method Man page
print,SelectVar-method Man page
print.SV Man page
ProyGroups Man page
ProyGroups<-,GroupProj-method Man page
ProyGroups,GroupProj-method Man page
QRO.Boot Man page
QRO.Boot<-,Bootstrap-method Man page
QRO.Boot,Bootstrap-method Man page
Ratios.Boot Man page
Ratios.Boot<-,Bootstrap-method Man page
Ratios.Boot,Bootstrap-method Man page
RQO Man page
RQO<-,DiStatis-method Man page
RQO,DiStatis-method Man page
RV Man page
RV<-,DiStatis-method Man page
RV,DiStatis-method Man page
RVPlot Man page
RVPlot,DiStatis-method Man page
SelectVar Man page
SelectVar-class Man page
SelectVar,DiStatis-method Man page
SelectVar-methods Man page
SortList Man page
SortList<-,GroupProj-method Man page
SortList,GroupProj-method Man page
Stability.Boot Man page
Stability.Boot<-,Bootstrap-method Man page
Stability.Boot,Bootstrap-method Man page
summary.Bootstrap Man page
summary,Bootstrap-method Man page
summary.DiStatis Man page
summary,DiStatis-method Man page
summary.GP Man page
summary,GroupProj-method Man page
summary,SelectVar-method Man page
summary.SV Man page
Table.Select Man page
Table.Select<-,SelectVar-method Man page
Table.Select,SelectVar-method Man page
Trajectories Man page
Trajectories<-,DiStatis-method Man page
Trajectories,DiStatis-method Man page
TrajPlot Man page
TrajPlot,DiStatis-method Man page
winesassesors Man page

Files

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.

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

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