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)