extractGateHistory {rflowcyt}R Documentation

Extracting the gating information from the history

Description

The history string corresponding to a specific gating Index specified by 'gateNum' is retrieved and output as a list of specific components.

Usage

extractGateHistory(x, gateNum)

Arguments

x a "FCSgate" object created after using createGate
gateNum the numeric column position of the gating index in the 'gate' matrix

Value

gateNum the numeric column position of the gating index in the 'gate' matrix
gateName character name of the gating index specified in the 'gate' matrix
type type of gating (ie, "biscut", "uniscut", "bipcut", "bidcut")
biscut.quadrant the quadrant specified (ie, ("+/+", "-/-", "+/-", "-/+"))
data.colpos the gated parameter column positions in the 'data' matrix
data.colnames the gated parameter column names in the 'data' matrix
IndexValue.In the value of the index that specifies inclusion or selection
gatingrange the vector of gating threshold(s)
prev.gateNum the previous or most prior gating index column position in the 'gate' matrix
prev.gateName the previous or most prior gating index column name in the 'gate' matrix
comment character string of the user-defined comment

Author(s)

A.J. Rossini and J.Y. Wan

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

FCS-class, FCSgate-class, createGate, \code{extractGatedData}

Examples

 if (require(rfcdmin)) {
      data.there<-is.element("MC.053",objects())
      if ((sum(data.there) != length(data.there))) {
        ## obtaining the FCS objects from VRC data
        data(MC.053min)
      }
  
####  foo1 : Gating type: uniscut, univariate single cut
foo1 <- createGate(MC.053, varpos=4, gatingrange=256,
                    type="uniscut", MY.DEBUG=TRUE)

#### foo2.3 : Gating type : biscut -/-
foo2.3 <- createGate(foo1, varpos=c(1,2),
                      gatingrange=c(256, 300),
                      type="biscut",
                      biscut.quadrant="-/-",
                      prev.gateNum=NULL,
                      MY.DEBUG=TRUE)

## obtain gate information for first uniscut gate
gate.info1<-extractGateHistory(foo1, gateNum=1)

## obtain gate information for the second biscut gate
gate.info2<-extractGateHistory(foo2.3, gateNum=2)

### foo2.3.1 : extraction
foo2.3.1 <- extractGatedData(foo2.3, gateNum=2,
                              IndexValue.In=1,
                              MY.DEBUG=TRUE)
## obtain the second biscut gate information after
## subset/extraction of row observations
gate.info2.1<-extractGateHistory(foo2.3.1, gateNum=2)
}

[Package rflowcyt version 1.2.0 Index]