countsTable: Extract the table of counts from a MIMOSA model

In MIMOSA: Mixture Models for Single-Cell Assays

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))

MIMOSA documentation built on Nov. 12, 2020, 2:02 a.m.