flowPlate-class: The flowPlate class.

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

Description

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.

Slots

plateName:

A character string containing the name of the plate.

plateSet:

A flowSet-class containing FCS event data. Prior to creating a flowPlate, the FCS files are first read into a flowSet-class using read.flowSet.

wellAnnotation:

A data.frame describing the layout of the plate. Each row describes one channel for a well.

Methods

[, [[

Subsetting. x[i] where i is either a scalar or character corresponding to a sample name, returns a flowPlate object, and x[[i]] a flowFrame object.

Usage:

flowSet[i]

flowSet[[i]]

Author(s)

Errol Strain, Florian Hahne, Perry Haaland

Examples

library(plateCore)
data(plateCore)

##Look at the wellAnnotation
wellAnnotation[1:4,]

## 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")

## Subset the flowPlate, creating another flowPlate
fpSmall <- fp["A01"]

## Extract a flowFrame from a flowPlate
ff <-fp[["A01"]]

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