MIMOSAExpressionSet {MIMOSA} | R Documentation |
Starting from a reshaped data frame in the correct format, construct an ExpressionSet object that can be used with MIMOSA.
MIMOSAExpressionSet(df, featureCols)
df |
a data.frame that is in the correct form |
featureCols |
the indices of the columns that identify features. |
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
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')