MIMOSA {MIMOSA} | R Documentation |
This method fits a MIMOSA model to count data stored in an ExpressionSet object.
MIMOSA(formula, data, ...)
formula |
describing the features on the lhs and the phenodata on the rhs, supporting extended formula interface with conditioning. |
data |
an |
... |
additional arguments |
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.
an object of type MIMOSAResult
MIMOSA-package
ConstructMIMOSAExpressionSet
MIMOSAResult
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')