countsTable {MIMOSA} | R Documentation

## Extract the table of counts from a MIMOSA model

### Description

Extract the table of counts from a MIMOSA model

### Usage

    countsTable(object, proportion = FALSE)

    ## S4 method for signature 'MIMOSAResult'
    countsTable(object, proportion = FALSE)

    ## S4 method for signature 'MCMCResult'
    countsTable(object, proportion = FALSE)

    ## S4 method for signature 'MDMixResult'
    countsTable(object, proportion = FALSE)

    ## S3 method for class 'MIMOSAResultList'
    countsTable(object, proportion = FALSE)

    ## S4 method for signature 'MIMOSAResultList'
    countsTable(object, proportion = FALSE)

### Arguments

`object` | a `MIMOSAResult`
`proportion` | `logical` return the counts or the proportions

### Value

a `data.frame` of counts to which the model was fit.

a `data.frame` of counts for the stimulated and unstimulated samples

### 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')
    head(countsTable(result))
    head(countsTable(result,proportion=TRUE))

[Package MIMOSA version 1.26.0 Index]