MIMOSAExpressionSet: Construct an ExpressionSet for MIMOSA

In RGLab/MIMOSA: Mixture Models for Single-Cell Assays

Description

Starting from a reshaped data frame in the correct format, construct an ExpressionSet object that can be used with MIMOSA.

Usage

MIMOSAExpressionSet(df, featureCols)

Arguments

df	a data.frame that is in the correct form
featureCols	the indices of the columns that identify features.

Details

The featureCols will be used to construct feature names, and these columns will be dropped from the exprs matrix. The column names are assumed to have names that contain '_' characters separating phenotypic characteristics. These would be generated automatically if the data frame was constrcuted with 'reshape'. They are used to construct the phenoData for the expression set

Examples

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')

RGLab/MIMOSA documentation built on Nov. 13, 2020, 5:04 a.m.