VRC.HVTNFCS {rflowcyt} | R Documentation

## Sequential Gating Scheme from Vaccine Research Center (VRC), NIH, Bethesda, MD; Mario Roederer, PhD

### 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

    VRC.HVTNFCS(myFCSobj, gate1.vars = c(1, 2), gate2.vars = c(7, 5),
                     gate3.vars = c(5, 3),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 cd4 variables for the second gate; default is column positions 7 and 5 respectively
`gate3.vars` | The vector of column variable positions corresponding to cd4 and cd8 variables for gate 3; default is column positions 5 and 3 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 proposed by Mario Roederer is the following:

gate1:bipcut:
  Forward Scatter VS Side Scatter (Select the lymphocytes–central cluster)
gate2:bidcut:
  cd3 VS cd4 (want cd3+ cells) (Select the cd3 positive cells on the right of the cutoff)
gate3:biscut:
  cd4 vs cd8 gate 3.1: (Select cd4+/cd8- cells) (+/- quadrant) gate 3.2: (Select cd4-/cd8+ cells) (-/+ quadrant)

In General, Types of Gating/Cutting:

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 `extractGateHistory` which extracts the gating information (eg. in order to obtain information about a previous gating index/column variable)

### Note

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

### Author(s)

A.J. Rossini & J.Y. Wan

### References

Mario Roederer, PhD

### See Also

`createGate`, `icreateGate`, `FHCRC.HVTNFCS`, `plotvar.FCS`, `extractGatedData`, `extractGateHistory`

### Examples

    if (require(rfcdmin)){

    data.there<-is.element(c("st.1829", "unst.1829", "st.DRT", "unst.DRT"),objects())
    if ( ( sum(data.there) != length(data.there) )){
    ## obtaining the FCS objects from VRC data
    data(VRCmin)
    }

    # HIV positive individual
    if (interactive()==TRUE){
    par(mfrow=c(4,2))
    st.DRT.VRC<-VRC.HVTNFCS(st.DRT)
    }

    }

[Package rflowcyt version 1.16.0 Index]