"FCSgate-class" {rflowcyt}R Documentation

Class "FCSgate" Flow Cytometry Standard extension to gating

Description

This class of objects extends the class FCS-class to incorporate information from gating which is a procedure by which rows or cells from the data are selected via one or two dimensional value restrictions or gating ranges.

Objects from the Class

Objects can be created by calls of the form new("FCSgate", ...). Essentially this new object includes the FCS-class object.

Slots

gate:
Object of class "matrix" containing the gating indices such that each column corresponds to a different gating procedure/index and the rows correspond to the positions of the original row/cell observations.
history:
Object of class "vector" containing the gating history strings such that each vector element corresponds to a different gating procedure/index and each string contains information about the particular gate, column variables that were used, and other additional comments.
extractGatedData.msg:
Object of class "vector" containing strings describing any extraction that took place corresponding to each gating procedure/index and history string; each string contains information about the particular corresponding gate column position and gate name and what value index was for inclusion/selection (ie, IndexValue.In)
current.data.obs:
Object of class "vector" contains the current data positional values from the original data
data:
Object of class "matrix" which holds integer data such that the columns are the variables (usually immunofluorescence measurements) and the rows are the cell observations.
metadata:
Object of class "FCSmetadata" which holds information about the file, data, and column variables among other items in the header of the original raw FCS binary file.

Extends

Class "FCS", directly.

Methods

No methods defined with class "FCSgate" in the signature.

Note

The methods createGate and icreateGate, functionally without plots or interactively with plots, respectively, extends the FCS-class to the FCSgate-class. Some interactive gating schemes are noted in FHCRC.HVTNFCS and VRC.HVTNFCS. Further testing after gating is implemented by runflowcytests on the particular variable of interest which is usually the Interferon Gamma Immunofluoroescence measurement.

Author(s)

A.J. Rossini, J.Y. Wan, and Zoe Moodie

References

Trevor Hastie, Robert Tibshirani, and Jerome Friedman. The Elements of Statistical Learning: Data Mining, Inference, and Prediction. Springer Series in Statistics : New York, 2001. pp.279-283.

Jerome H. Friedman and Nicholas I. Fisher. Bump Hunting in High-Dimensional Data. Tech Report. October 28, 1998.

J. Paul Robinson, et al. Current Protocols in Cytometry. John Wiley & Sons, Inc : 2001.

Mario Roederer and Richard R. Hardy. Frequency Difference Gating: A Multivariate Method for Identifying Subsets that Differe between Samples. Cytometry, 45:56-64, 2001.

Mario Roederer and Adam Treister and Wayne Moore and Leonore A. Herzenberg. Probability Binning Comparison: A Metric for Quantitating Univariate Distribution Differences. Cytometry, 45:37-46, 2001.

Keith A. Baggerly. Probability Binning and Testing Agreement between Multivariate Immunofluorescence Histograms: Extending the Chi-Squared Test. Cytometry, 45:141-150, 2001.

See Also

createGate, icreateGate, extractGatedData, extractGateHistory, FHCRC.HVTNFCS, VRC.HVTNFCS, "FCS-class", runflowcytests

Examples

default.FCSgateobj<-new("FCSgate")

[Package rflowcyt version 1.14.0 Index]