FHCRC.HVTNFCS {rflowcyt} | R Documentation |
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.
FHCRC.HVTNFCS(myFCSobj, gate1.vars = c(1, 2), gate2.vars = c(5, 7), gate3.vars = c(3, 4),MY.DEBUG = FALSE)
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 |
The Selection Sequence made by Julie McElrath's Lab is the following:
In General, the types of Gating/Cutting that are used in this gating scheme are the following:
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 |
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
The "FHCRC" data from the rfcdorig package can be used for this sequential gating scheme.
A.J. Rossini and J.Y. Wan
Julie McElrath, PhD
createGate
, icreateGate
,
showgate.FCS
,
VRC.HVTNFCS
, plotvar.FCS
,
"[-methods"
, "[[-methods"
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) } }