summaryStats-methods: Compute summary statistics on a flowPlate

In plateCore: Statistical tools and data structures for plate-based flow cytometry

Description

This function computes the median fluorescence intensity (MFI) and the MFI ratio (ratio of test well MFI to negative control MFI) for each well/channel in a flowPlate. The predicted percent positive (Predict.PP) and gate score (Gate.Score) come from a robust logistic regression of the MFI ratio to either the percentage of positive cells or the actual count of positive cells. Predict.PP is the estimated percent positive based on the MFI ratio and Gate.Score is the number of standardized residuals the sample data point is away from the best fit line. The glmrob function from the robustbase package is used for the regression. Results from summaryStats are stored in the wellAnnotation data.fame.

Usage

summaryStats(data, Events="Percentage", ...)

Arguments

data	A flowPlate
Events	The robust logistic regression can be performed using either the percentage of events above the negative control gate ("Percentage") or the actual number of events above the gate ("Actual").
...	optional arguments

Value

Returns a flowPlate

Author(s)

Errol Strain

Examples

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")
fp <- applyControlGates(fp,gateType="Negative.Control")

# Compute summary statistics
fp <- summaryStats(fp)

# There should now be MFI and MFI.ratio columns in the wellAnnotation
head(wellAnnotation(fp))

plateCore documentation built on May 6, 2019, 2:41 a.m.