MIMOSAExpressionSet {MIMOSA} | R Documentation

## Construct an ExpressionSet for MIMOSA

### Description

Starting from a reshaped data frame in the correct format, construct an ExpressionSet object that can be used with MIMOSA.

### Usage

    MIMOSAExpressionSet(df, featureCols)

### Arguments

`df` | a data.frame that is in the correct form
`featureCols` | the indices of the columns that identify features.

### Details

The featureCols will be used to construct feature names, and these columns will be dropped from the exprs matrix. The column names are assumed to have names that contain '_' characters separating phenotypic characteristics. These would be generated automatically if the data frame was constrcuted with 'reshape'. They are used to construct the phenoData for the expression set

### Examples

    E<-ConstructMIMOSAExpressionSet(ICS,
      reference=ANTIGEN%in%'negctrl',measure.columns=c('CYTNUM','NSUB'),
      other.annotations=c('CYTOKINE','TCELLSUBSET','ANTIGEN','UID'),
      default.cast.formula=component~UID+ANTIGEN+CYTOKINE+TCELLSUBSET,
      .variables=.(TCELLSUBSET,CYTOKINE,UID),
      featureCols=1,ref.append.replace='_REF')

[Package MIMOSA version 1.16.1 Index]