MAST (version 0.931)

FluidigmAssay: Constructor for a FluidigmAssay

Description

Constructs a FluidigmAssay object. Differs little from the SingleCellAssay constructor. Only the ncells parameter is additionally required.

Usage

FluidigmAssay(dataframe = NULL, idvars, primerid, measurement, ncells,
  geneid = 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

ncells

A character specifying the column which gives the number of cells per well

geneid

An optional character alternate id for primers.

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

A FluidigmAssay object

Examples

# NOT RUN {
data(vbeta)
colnames(vbeta)
vbeta <- computeEtFromCt(vbeta)
vbeta.fa <- FluidigmAssay(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')
show(vbeta.fa)
nrow(vbeta.fa)
ncol(vbeta.fa)
head(fData(vbeta.fa)$primerid)
table(cData(vbeta.fa)$Subject.ID)
vbeta.sub <- subset(vbeta.fa, Subject.ID=='Sub01')
show(vbeta.sub)
# }