plateCore (version 1.30.0)

plateCore-package: plateCore: A Bioconductor package for high throughput analysis of flow cytometry data

Description

plateCore is a Bioconductor packaged created to make processing and analysis of large, complex flow datasets in R easier. High throughput flow studies are often run in a 96 or 384-well plate format, with a number of different samples, controls, and antibodies-dye conjugates present on the plate. Analyzing the output from the cytometer requires keeping track of the contents of each well, matching sample wells with control wells, gating each well/channel separately, making the appropriate plots, and summarizing the results. plateCore extends the flowCore and flowViz packages to work on flowPlate objects that represent these large flow datasets. For those familiar with flowCore and flowViz, the gating (filtering), transformation, and other data manipulations for flowPlates are very similar to flowSets.

Details

Package:

plateCore

Type:

Package

Version:

1.2.1

Date:

2009-06-29

References

Insert flowCore and flowViz publications.

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 object from the platePBMC and the wellAnnotation
fp <- flowPlate(pbmcPlate,wellAnnotation,plateName="P1")