SingleCellAssay (version 0.80)

SingleCellAssay: SingleCellAssay: A constructor for an object of type SingleCellAssay.

Description

This is the constructor for the class. This class intends to ease the analysis of single cell assays, in which multiple, exchangeable, cells from an experimental unit (patient, or organism) are assayed along several (or many) dimensions, such as genes. A few examples of this might be Fluidigm gene expression chips, or single cell sequencing experiments. The chief functionality is to make it easy to keep cellular-level metadata linked to the measurements through cellData and phenoData. There are also subsetting and splitting measures to coerce between a SingleCellAssay, and a SCASet.

Usage

SingleCellAssay(dataframe = NULL, idvars = NULL, primerid = NULL,
  measurement = NULL, id = numeric(0), cellvars = NULL,
  featurevars = NULL, phenovars = NULL, ...)

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

...

additional arguments are ignored

Value

SingleCellAssay object

See Also

FluidigmAssay

Examples

# NOT RUN {
## See FluidigmAssay for examples
# }
# NOT RUN {
example(FluidigmAssay)
# }