countsTable {MIMOSA} | R Documentation |
Extract the table of counts from a MIMOSA model
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)
object |
a |
proportion |
|
a data.frame
of counts to which the model was fit.
a data.frame
of counts for the stimulated and unstimulated samples
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))