FromFlatDF {MAST} | R Documentation |
SingleCellAssay are a generic container for such data and are simple wrappers around SummarizedExperiment objects. Subclasses exist that embue the container with additional attributes, eg FluidigmAssay.
FromFlatDF( dataframe, idvars, primerid, measurement, id = numeric(0), cellvars = NULL, featurevars = NULL, phenovars = NULL, class = "SingleCellAssay", check_sanity = TRUE, ... )
dataframe |
A 'flattened' |
idvars |
character vector naming columns that uniquely identify a cell |
primerid |
character vector of length 1 that names the column that identifies what feature (i.e. gene) was measured |
measurement |
character vector of length 1 that names the column containing the measurement |
id |
An identifier (eg, experiment name) for the resulting object |
cellvars |
Character vector naming columns containing additional cellular metadata |
featurevars |
Character vector naming columns containing additional feature metadata |
phenovars |
Character vector naming columns containing additional phenotype metadata |
class |
desired subclass of object. Default |
check_sanity |
(default: |
... |
additional arguments are ignored |
SingleCellAssay, or derived, object
data(vbeta) colnames(vbeta) vbeta <- computeEtFromCt(vbeta) vbeta.fa <- FromFlatDF(vbeta, idvars=c("Subject.ID", "Chip.Number", "Well"), primerid='Gene', measurement='Et', ncells='Number.of.Cells', geneid="Gene",cellvars=c('Number.of.Cells', 'Population'), phenovars=c('Stim.Condition','Time'), id='vbeta all', class='FluidigmAssay') show(vbeta.fa) nrow(vbeta.fa) ncol(vbeta.fa) head(mcols(vbeta.fa)$primerid) table(colData(vbeta.fa)$Subject.ID) vbeta.sub <- subset(vbeta.fa, Subject.ID=='Sub01') show(vbeta.sub)