extractGateHistory {rflowcyt} | R Documentation |
The history string corresponding to a specific gating Index specified by 'gateNum' is retrieved and output as a list of specific components.
extractGateHistory(x, gateNum)
x |
a "FCSgate" object created after using createGate |
gateNum |
the numeric column position of the gating index in the 'gate' matrix |
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 |
A.J. Rossini and J.Y. Wan
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.
FCS-class
, FCSgate-class
,
createGate, \code{extractGatedData}
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) }