Select a subset of events in a flowPlate. If a flowPlate and filter are supplied, then this function calls the Subset function from flowCore. Additionally, the plateCore version of Subset also makes it easy to filter individual flowFrames and keep the flowPlate structure.
Once setControlGates has been used to create gates for a flowPlate object, gates are applied to test samples using applyControlGates. The applyControlGates function is separated from setControlGates since gates may need be changed outside of setControlGates.
compensate
(Package: plateCore) :
Compensate a flowPlate to correct for the effects of spillover.
Flow samples are often stained with multiple types of fluorophores. Unfortunately, the emission spectra for these different fluorophores often overlap, and the signals must be corrected before proceeding with the analysis. Compensate adjusts for spillover using the method implemented in the package flowCore. Unlike flowCore, compensate only adjusts for the dyes/fluorophores listed in wellAnnotation.
This function is a modified version of densityplot from the flowViz package that allows for multiple flowFrames per panel. flowViz densityplot plots the density curves in a one per panel style, while the flowPlate densityplot can overlay densities.
fixAutoFl
(Package: plateCore) :
Correct for the effects of cell size (FSC) on autofluorescence
The fixAutoFl function uses the method of Hahne et al. 2006 (Genome Biology) to fit a robust, log-log linear regression to the fluorescence channel of interest versus forward scatter (FSC). The current implementation scales the corrected data so the median fluorescence intensity (MFI) is the same before and after fixAutoFl.
flowPlates are the basic data containers for the plateCore package. A flowPlate is essentially a flowSet-class, plus a data.frame describing the layout of the plate and contents of individual wells.
Constructor for a flowPlate object. sampleNames for the flowSet should match the Well.Id column of wellAnnotation. Well.Ids must be unique to sampleNames, which is usually ensured by using the 3 character designations for wells (e.g. "A01","A02",...,"H12").
fpbind
(Package: plateCore) :
Merge multiple flowPlates into a single virtual flowPlate
A function to combine multiple flowPlates into a single flowPlate object. The plateName identifiers for the flowPlates must be unique within the set to be bound, otherwise the bind will fail.
A Quality Control plot to check the number of events in each channel that are at either their minimum or maximum value. A large number of these events may indicate a problem with the sample.
providing 
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