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 1.16.0 Index]