Construct a SingleCellAssay (or derived subclass) from a 'flat' (melted) data.frame/data.table

Share:

Description

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.

Usage

1
2
3
4
5
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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
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)

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.