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]