| cytoFrame-class {prada} | R Documentation |
This class represents the data contained in a FCS 3.0 file or similar data structures.
Although objects of class cytoFrame can be used to hold arbitrary
data of cell populations, the main focus lies on flow-cytometry data.
FCS 3.0 is the Data File Standard for Flow Cytometry, Version FCS3.0. See the vignette of this package for additional information on using the object system for handling of flow-cytometry data.
Objects can be created using
new('cytoFrame,
exprs = ...., # Object of class matrix
description = .... # Object of class character
)
or the function readFCS.
exprs:matrix containing
the measured intensities. Rows correspond to cells, columns to the
different channels. The colnames attribute of the matrix is
supposed to hold the names or identifiers for the channels. The
rownames attribute would usually not be set.description:well:cytoSet collection and will usually
be filled in by the function readCytoSet.gate:gateSet. This object can be used to
select defined subsets of the data, a process referred to as
gating in the analysis of flow-cytometry data.cytoFrame.
The subsetting is applied to the exprs slot, while the
description slot is unchanged.cytoFrame objects. The additional
argument gate can be used to plot subsets of the data defined by
either an object of class gate or by a character
vector giving the name of one of the gates in the list.gate or
gateSet based on a selection made from the
data. See gateMatrix for further details.Florian Hahne, Wolfgang Huber
readFCS,
cytoSet, gate,
gateSet, gateMatrix
intens <- matrix(runif(100), ncol=4)
colnames(intens) <- c("FL1-H", "FL2-H", "FL3-H", "FL4-H")
a <- new("cytoFrame",
exprs=intens,
description=c(name="example data", date=date()))
description(a)
dim(exprs(a))
a[1:3, -4]
plot(a)
## Not run:
g1 <- drawGate(a, name="Gate1")
## End(Not run)