flowFrame-class {flowCore}R Documentation

'flowFrame': a class for storing observed quantitative properties for a population of cells from a FACS run

Description

This class represents the data contained in a FCS 3.0 file or similar data structures.

Details

Objects of class flowFrame can be used to hold arbitrary data of cell populations, acquired in flow-cytometry.

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.

Creating Objects

Objects can be created using
new("flowFrame",
exprs = ...., Object of class matrix
parameters = ...., Object of class AnnotatedDataFrame
description = ...., Object of class list
)
or the function read.FCS.

Slots

exprs:
Object of class 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.
parameters:
An AnnotatedDataFrame containing information about each column of the flowFrame. This will generally be filled in by read.FCS or similar functions using data from the description slot that describes the parameters.
description:
A list containing the meta data included in the FCS file.

Methods

[
subsetting. Returns an object of class flowFrame. The subsetting is applied to the exprs slot, while the description slot is unchanged.
$
subsetting by channel name.
exprs, exprs<-
extract or replace the intensities.
description
extract the description.
parameters
extract parameters and returns object of class AnnotatedDataFrame
compensate
apply a compensation matrix on a flowFrame object.
transform
apply a transformation function on a flowFrame object.
filter
apply a filter object on a flowSet object. See filter for details
show
display summary.
plot
scatterplot for flowFrame objects.
ncol,nrow
extract the dimensions of the data matrix.
keyword
extract one or more entries from the description slot by keyword
spillover
extract spillover matrix from description slot if present
split
split flowFrame object according to a filter or gate.
identifier
extract GUID. Returns file name if not available. See identifier for details.
featureNames
extract parameter description.
each_row, each_col
apply function over rows or columns of the data matrix.
names
names of the monitored channels
summary
Return descriptive statistical summary (min, max, mean and quantile) for each channel
Subset
Subset a flowFrame
==
Test equality between flowFrame

Author(s)

F. Hahne, B. Ellis, P. Haaland and N. Le Meur


[Package flowCore version 1.0.2 Index]