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", ...)

FluidigmAssay(...)

Arguments

dataframe
A 'flattened' data.frame or data.table containing columns giving cell and feature identifiers and a measurement column
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
character providing desired subclass to construct.
...
additional arguments are ignored

Value

SingleCellAssay, or derived, object

Examples

data(vbeta) colnames(vbeta)
#> [1] "Sample.ID" "Subject.ID" "Experiment.Number" #> [4] "Chip.Number" "Stim.Condition" "Time" #> [7] "Population" "Number.of.Cells" "Well" #> [10] "Gene" "Ct"
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)
#> class: FluidigmAssay #> dim: 75 456 #> metadata(0): #> assays(1): Et #> rownames(75): B3GAT1 BAX ... TNFRSF9 TNFSF10 #> rowData names(2): Gene primerid #> colnames(456): Sub01 1 A01 Sub01 1 A02 ... Sub02 3 H10 Sub02 3 H11 #> colData names(9): Number.of.Cells Population ... Time wellKey
nrow(vbeta.fa)
#> [1] 75
ncol(vbeta.fa)
#> [1] 456
head(mcols(vbeta.fa)$primerid)
#> [1] "B3GAT1" "BAX" "BCL2" "CCL2" "CCL3" "CCL4"
table(colData(vbeta.fa)$Subject.ID)
#> #> Sub01 Sub02 #> 177 279
vbeta.sub <- subset(vbeta.fa, Subject.ID=='Sub01') show(vbeta.sub)
#> class: FluidigmAssay #> dim: 75 177 #> metadata(0): #> assays(1): Et #> rownames(75): B3GAT1 BAX ... TNFRSF9 TNFSF10 #> rowData names(2): Gene primerid #> colnames(177): Sub01 1 A01 Sub01 1 A02 ... Sub01 2 H09 Sub01 2 H10 #> colData names(9): Number.of.Cells Population ... Time wellKey