MIMOSA {MIMOSA} | R Documentation

## Fit a MIMOSA Model

### Description

This method fits a MIMOSA model to count data stored in an ExpressionSet object.

### Usage

    MIMOSA(formula, data, ...)

### Arguments

`formula` | describing the features on the lhs and the phenodata on the rhs, supporting extended formula interface with conditioning.
`data` | an `ExpressionSet` object with features on rows and samples (labelled with phenoData) on columns.
`...` | additional arguments

### Details

The ExpressionSet should be fully annotated with featureData and phenoData. For ICS data, for example, features would be positive and negative counts for different cytokine producing cell subsets (i.e. IFNg_pos, IFNg_neg) The formula lhs should contain features and the rhs should contain phenotypic variable. See the vignette for an example.

### Value

an object of type `MIMOSAResult`

### See Also

`MIMOSA-package` `ConstructMIMOSAExpressionSet` `MIMOSAResult`

### Examples

    data(ICS)
    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')

    result<-MIMOSA(NSUB+CYTNUM~UID+TCELLSUBSET+CYTOKINE|ANTIGEN,
        data=E, method='EM',
        subset=RefTreat%in%'Treatment'&ANTIGEN%in%'ENV',
        ref=ANTIGEN%in%'ENV'&RefTreat%in%'Reference')

[Package MIMOSA version 1.20.1 Index]