FHCRC.HVTNFCS {rflowcyt}R Documentation

Fred Hutchinson Cancer Research Center Sequential Gating Procedure proposed by Julie McElrath's Lab

Description

This function uses icreateGate and createGate to select the datapoints which are of particular interest. The selection process is realized in an index column which is added to the data of the FCS object. In particular, after a series of gating/datapoint selection sequences, the interferon gamma variable is of interest.

To row reduce the data of the FCS object, the function, extractGatedData should be used on the last gate index to obtain the rows/cells and then should be used again to subset across columns to obtain the gamma interferon column.

Usage


FHCRC.HVTNFCS(myFCSobj, gate1.vars = c(1, 2), gate2.vars = c(5, 7),
                 gate3.vars = c(3, 4),MY.DEBUG = FALSE)

Arguments

myFCSobj a FCS object
gate1.vars The vector of column variable positions corresponding to Forward Scatter and Side Scatter variables for the first gate; default is column positions 1 and 2 respectively
gate2.vars The vector of column variable positions corresponding to cd3 and cd8 variables for the second gate; default is column positions 5 and 7 respectively
gate3.vars The vector of column variable positions corresponding to cd69 and Interferon Gamma variables for gate 3; default is column positions 3 and 4 respectively
MY.DEBUG if TRUE, then will print the debugging statements; otherwise, if FALSE, then will surpress the debugging statements; default is FALSE

Details

The Selection Sequence made by Julie McElrath's Lab is the following:

gate1:bidcut:
Forward Scatter VS Side Scatter
single gate
(Select the lymphocytes–central cluster)
gate2:bidcut:
cd3 VS cd8
gate 2.1:
(Select cd3+/cd8-)
gate 2.2:
(Select cd3+/cd8+)
gate3:biscut:
cd69 vs Interferon Gamma
gate 3.1:
(Select +/+ which are the cd4+ cells (from gate2.1))
gate 3.2:
(Select +/+ which are the cd8+ cells (from gate2.2))

In General, the types of Gating/Cutting that are used in this gating scheme are the following:

uniscut = univariate single cut
(Selection of the positive/right half)
biscut = bivariate single cut
(Selection of the +/-, -/-. +/+, or -/+ quadrant)
bidcut = bivariate double cut
(Selection of the center rectangle that results)

Value

FCS object with the following slots:
data A augmented dataframe with the added-on gating column variables/indices
metadata a FCSmetadata object with the information about the gating column variables: $PnR (gating range), $PnN (gating variable's shortname/unused name in the data of the FCS object), $PnS (gating variable's longname/used name), and other slot information

WARNING

This gating scheme is not standard, and there may have been changes to the gating scheme. This gating scheme only serves as an example, which demonstrates the use of createGate,icreateGate and "[[-methods" which extracts the metadata information (eg. in order to obatin information about a previous gating index/column variable

Note

The "FHCRC" data from the rfcdorig package can be used for this sequential gating scheme.

Author(s)

A.J. Rossini and J.Y. Wan

References

Julie McElrath, PhD

See Also

createGate, icreateGate, showgate.FCS, VRC.HVTNFCS, plotvar.FCS, "[-methods", "[[-methods"

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)
    }

    if (interactive()==TRUE){
      par(mfrow=c(4,2))

      MC.053.FHCRC<-FHCRC.HVTNFCS(MC.053)
    }
  }


[Package rflowcyt version 1.4.0 Index]