Partial LeAst Squares for Multiomic Analysis

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Documentation for package ‘plasma’ version 1.1.3

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

assemble	Esophageal carcinoma (ESCA) data or lung squamous cell carcinoma (LUSC) data from The Cancer Genome Atlas (TCGA).
barplot-method	Class '"plasma"'
combineAllWeights	Class '"CombinedWeights"'
CombinedWeights	Class '"CombinedWeights"'
CombinedWeights-class	Class '"CombinedWeights"'
Contribution	Class '"Contribution"'
Contribution-class	Class '"Contribution"'
fitCoxModels	Class '"MultiplePLSCoxModels"'
fitSingleModel	Class '"SingleModel"'
getAllWeights	Class '"Contribution"'
getCompositeWeights	Class '"Contribution"'
getFinalWeights	Class '"Contribution"'
getSizes	Class '"MultiplePLSCoxModels"'
getTop	Class '"Contribution"'
heat	Class '"Contribution"'
heat-method	Class '"Contribution"'
image-method	Class '"Contribution"'
image-method	Class '"CombinedWeights"'
interpret	Class '"CombinedWeights"'
loadESCAdata	Esophageal carcinoma (ESCA) data or lung squamous cell carcinoma (LUSC) data from The Cancer Genome Atlas (TCGA).
loadLUSCdata	Esophageal carcinoma (ESCA) data or lung squamous cell carcinoma (LUSC) data from The Cancer Genome Atlas (TCGA).
m450info	Esophageal carcinoma (ESCA) data or lung squamous cell carcinoma (LUSC) data from The Cancer Genome Atlas (TCGA).
meanModeImputer	Imputation
mirESCA	ESCA type data
MultiOmics	Class '"MultiOmics"'
MultiOmics-class	Class '"MultiOmics"'
MultiplePLSCoxModels	Class '"MultiplePLSCoxModels"'
MultiplePLSCoxModels-class	Class '"MultiplePLSCoxModels"'
Outcome	Esophageal carcinoma (ESCA) data or lung squamous cell carcinoma (LUSC) data from The Cancer Genome Atlas (TCGA).
pickSignificant	Class '"Contribution"'
plasma	Class '"plasma"'
plasma-class	Class '"plasma"'
plasmaEnv	Esophageal carcinoma (ESCA) data or lung squamous cell carcinoma (LUSC) data from The Cancer Genome Atlas (TCGA).
plasmaPredictions	Class '"plasmaPredictions"'
plasmaPredictions-class	Class '"plasmaPredictions"'
plot-method	Class '"MultiOmics"'
plot-method	Class '"SingleModel"'
plot-method	Class '"MultiplePLSCoxModels"'
plot-method	Class '"plasma"'
plot-method	Class '"plasmaPredictions"'
predict-method	Class '"SingleModel"'
predict-method	Class '"MultiplePLSCoxModels"'
predict-method	Class '"plasma"'
prepareMultiOmics	Class '"MultiOmics"'
samplingImputer	Imputation
SingleModel-class	Class '"SingleModel"'
stdize	Class '"CombinedWeights"'
summary-method	Class '"MultiOmics"'
summary-method	Class '"SingleModel"'
summary-method	Class '"MultiplePLSCoxModels"'
summary-method	Class '"plasma"'
summary-method	Class '"Contribution"'
summary-method	Class '"CombinedWeights"'
TCGA-ESCA	Esophageal carcinoma (ESCA) data or lung squamous cell carcinoma (LUSC) data from The Cancer Genome Atlas (TCGA).
TCGA-LUSC	Esophageal carcinoma (ESCA) data or lung squamous cell carcinoma (LUSC) data from The Cancer Genome Atlas (TCGA).
tfESCA	ESCA type data
validMultiOmics	Class '"MultiOmics"'
validMultipleCoxModels	Class '"MultiplePLSCoxModels"'
[-method	Class '"MultiOmics"'
[-method	Class '"MultiplePLSCoxModels"'
[-method	Class '"Contribution"'