CyData-getset {cydar}R Documentation

CyData getters and setters

Description

Methods to get and set data slots in the CyData object.

Usage

## S4 method for signature 'CyData'
markerData(x)
## S4 replacement method for signature 'CyData'
markerData(x) <- value

## S4 method for signature 'CyData'
intensities(x)
## S4 replacement method for signature 'CyData'
intensities(x) <- value

## S4 method for signature 'CyData'
cellAssignments(x)
## S4 replacement method for signature 'CyData'
cellAssignments(x) <- value

## S4 method for signature 'CyData'
cellIntensities(x)
## S4 replacement method for signature 'CyData'
cellIntensities(x) <- value

## S4 method for signature 'CyData'
cellData(x)
## S4 replacement method for signature 'CyData'
cellData(x) <- value

## S4 method for signature 'CyData'
nmarkers(x)
## S4 method for signature 'CyData'
ncells(x)

## S4 method for signature 'CyData'
markernames(object)
## S4 replacement method for signature 'CyData'
markernames(object) <- value

## S4 method for signature 'CyData'
sampleNames(object)
## S4 replacement method for signature 'CyData'
sampleNames(object) <- value

Arguments

x, object

A CyData object.

value

For markernames and sampleNames, a character vector specifying the names of the markers and samples, respectively. Otherwise, an appropriate object to use to replace the corresponding slot of x.

Details

markerData, intensities, cellAssignments, cellIntensities and cellData are methods to get or set the slots in a CyData object. general, setting should not be performed unless adding annotation for particular markers or cells (or if you really know what you're doing). Caution is especially advised when using cellIntensities<- and/or cellData<-, as several methods in this package rely on a particular ordering of cells.

Several convenience functions are also provided. nmarkers will return the number of markers, while ncells will return the number of cells. markernames will return the marker names (i.e., the row names of markerData), while sampleNames will return the sample names (i.e., the column names of object). The respective replacement functions will modify these names.

Value

For the setters, a new CyData object will be generated with modified entries for the appropriate slots. For the getters, an object of the class corresponding to each slot will be returned. nmarkers and ncells will return integer scalars, while markerNames and sampleNames will return character vectors.

Author(s)

Aaron Lun

Examples

example(CyData) # Mocking up an object.

nmarkers(cyd)
markernames(cyd)
sampleNames(cyd)

markerData(cyd)
markerData(cyd)$stuff <- runif(nmarkers(cyd))
markerData(cyd)

head(intensities(cyd))
cellIntensities(cyd)[,1:10]

[Package cydar version 1.4.0 Index]