'cytoSet': a class for storing raw data from a quantitative cell-based assay

Description

This class is a container for a set of cytoFrame objects

Usage

## S4 method for signature 'cytoSet':
phenoData(object)
\S4method{phenoData<-}{cytoSet,ANY}(object,value)
## S4 method for signature 'cytoSet':
pData(object)
## S4 method for signature 'cytoSet':
colnames(object)
\S4method{colnames<-}{cytoSet,ANY}(object,value)
## S4 method for signature 'cytoSet':
show(object)
\S4method{[}{cytoSet,ANY}(x, i)
\S4method{[[}{cytoSet,ANY}(x, i)

Arguments

Creating Objects

Objects can be created using the function readCytoSet or via
new('cytoSet,
frames = ...., # environment with cytoFrames
phenoData = .... # object of class phenoData
colnames = .... # object of class character
)

Slots

frames:

An environment containing one or more cytoFrame objects.

phenoData:

A phenoData. Each row corresponds to one of the cytoFrames in the frames slot. It is mandatory that the pData has column named name

colnames:

A character object with the (common) column names of all the data matrices in the cytoFrames.

Methods

[, [[

subsetting. If x is cytoSet, then x[i] returns a cytoSet object, and x[[i]] a cytoFrame object. The semantics is similar to the behavior of the subsetting operators for lists.

colnames, colnames<-

extract or replace the colnames slot.

phenoData, phenoData<-

extract or replace the phenoData slot.

show

display summary.

Author(s)

Wolfgang Huber

See Also

readCytoSet, cytoFrame-class

Examples

cset<-readCytoSet(path=system.file("extdata", package="prada"),
  pattern="[A-Z][0-9][0-9]$")
cset
pData(cset)
cset[[1]]
cset[["fas Bcl2 plate323-04-04.A02"]]
cset["fas Bcl2 plate323-04-04.A02"]
cset[1:3]

cset[[1]] <- exprs(cset[[1]])[1:100, ]