Description Usage Arguments Value Author(s) Examples
A function to estimate the threshold between positive and negative cells. This threshold corresponds to
a one-dimensional gate, and cells above the gate are considered positive.
The default value of numMads=5
generally works well on the
linear scale, but will need to be adjusted for transformed data. If each well
contains a large number of events for the cell type of interest (>1000), then
using the 99.5th quantile usually gives similar values.
1 | setControlGates(data, gateType, threshType="MAD", numMads=5, isoquantile=.995, ...)
|
data |
A |
gateType |
The type of gate to be set. Currently only "Negative.Control" gates are supported. |
threshType |
Values can be either "MAD", for median absolute deviation based gating, or "isoQuant" for quantile based gating. |
numMads |
Number of median absolute deviations above the median to set the initial gate. |
isoquantile |
Quantile setting for "isoQuant" threshType. |
... |
optional arguments. |
Returns a flowPlate
Errol Strain
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | library(plateCore)
data(plateCore)
## Get the lymphocytes
rectGate <- rectangleGate("FSC-H"=c(300,700),"SSC-H"=c(50,400))
pbmcPlate <- Subset(pbmcPlate, rectGate)
# Create a flowPlate from the sample data in plateCore
fp <- flowPlate(pbmcPlate,wellAnnotation,plateName="P1")
# Create a set of negative control gates and then apply them
fp <- setControlGates(fp,gateType="Negative.Control")
# There should now be a Negative.Control.Gate column in wellAnnotation
head(wellAnnotation(fp))
|
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