epheno: epheno object.

In phenoTest: Tools to test association between gene expression and phenotype in a way that is efficient, structured, fast and scalable. We also provide tools to do GSEA (Gene set enrichment analysis) and copy number variation.

Description

Object obatined with ExpressionPhenoTest function.

Usage

data(epheno)

Format

The format is: Formal class 'epheno' [package "phenoTest"] with 8 slots ..@ p.adjust.method : chr "none" ..@ assayData :<environment: 0x1050d5a78> ..@ phenoData :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots .. .. ..@ varMetadata :'data.frame': 5 obs. of 1 variable: .. .. .. ..$ labelDescription: chr [1:5] NA NA NA NA ... .. .. ..@ data :'data.frame': 12 obs. of 5 variables: .. .. .. ..$ phenoName : Factor w/ 3 levels "lymph.node.status",..: 3 3 3 3 3 1 1 1 2 3 ... .. .. .. ..$ phenoClass: Factor w/ 3 levels "categorical",..: 2 2 2 2 2 1 1 1 3 2 ... .. .. .. ..$ phenoType : Factor w/ 3 levels "mean","pval",..: 1 1 1 3 3 1 1 3 3 2 ... .. .. .. ..$ meanLabel : Factor w/ 5 levels "[45.2,49.2)",..: 1 2 3 NA NA 4 5 NA NA NA ... .. .. .. ..$ survTime : Factor w/ 1 level "Months2Relapse": NA NA NA NA NA NA NA NA 1 NA ... .. .. ..@ dimLabels : chr [1:2] "sampleNames" "sampleColumns" .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots .. .. .. .. ..@ .Data:List of 1 .. .. .. .. .. ..$ : int [1:3] 1 1 0 ..@ featureData :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots .. .. ..@ varMetadata :'data.frame': 0 obs. of 1 variable: .. .. .. ..$ labelDescription: chr(0) .. .. ..@ data :'data.frame': 1000 obs. of 0 variables .. .. ..@ dimLabels : chr [1:2] "featureNames" "featureColumns" .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots .. .. .. .. ..@ .Data:List of 1 .. .. .. .. .. ..$ : int [1:3] 1 1 0 ..@ experimentData :Formal class 'MIAME' [package "Biobase"] with 13 slots .. .. ..@ name : chr "" .. .. ..@ lab : chr "" .. .. ..@ contact : chr "" .. .. ..@ title : chr "" .. .. ..@ abstract : chr "" .. .. ..@ url : chr "" .. .. ..@ pubMedIds : chr "" .. .. ..@ samples : list() .. .. ..@ hybridizations : list() .. .. ..@ normControls : list() .. .. ..@ preprocessing : list() .. .. ..@ other : list() .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots .. .. .. .. ..@ .Data:List of 1 .. .. .. .. .. ..$ : int [1:3] 1 0 0 ..@ annotation : chr "hgu133a" ..@ protocolData :Formal class 'AnnotatedDataFrame' [package "Biobase"] with 4 slots .. .. ..@ varMetadata :'data.frame': 0 obs. of 1 variable: .. .. .. ..$ labelDescription: chr(0) .. .. ..@ data :'data.frame': 12 obs. of 0 variables .. .. ..@ dimLabels : chr [1:2] "sampleNames" "sampleColumns" .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots .. .. .. .. ..@ .Data:List of 1 .. .. .. .. .. ..$ : int [1:3] 1 1 0 ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots .. .. ..@ .Data:List of 4 .. .. .. ..$ : int [1:3] 2 12 0 .. .. .. ..$ : int [1:3] 2 10 0 .. .. .. ..$ : int [1:3] 1 3 0 .. .. .. ..$ : int [1:3] 1 0 0

Examples

data(epheno)
## maybe str(epheno) ; plot(epheno) ...

phenoTest documentation built on Nov. 8, 2020, 7:53 p.m.