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 1.4.0 Index]