Description Usage Arguments Details Examples
Starting from a reshaped data frame in the correct format, construct an ExpressionSet object that can be used with MIMOSA.
1 | 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
1 2 3 4 5 6 | 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')
|
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anyDuplicated, append, as.data.frame, basename, cbind, colnames,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which.max, which.min
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