CyData-getset {cydar} | R Documentation |
Methods to get and set data slots in the CyData object.
## 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
x, object |
A CyData object. |
value |
For |
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.
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.
Aaron Lun
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]