BASiCS (version 0.3.1)

BASiCS_Data-methods: S4 methods for BASiCS_Data objects

Description

S4 methods for BASiCS_Data-class objects.

Usage

# S4 method for BASiCS_Data
show(object)
# S4 method for BASiCS_Data
counts(object, type = "all")
# S4 method for BASiCS_Data
displaySpikeInput(object)
# S4 method for BASiCS_Data
displayTechIndicator(object)
# S4 method for BASiCS_Data
displayGeneNames(object)
# S4 method for BASiCS_Data
displayBatchInfo(object)

Arguments

object

A BASiCS_Data object.

type

Only required for counts method. A string indicating which genes are returned.

Value

show

Prints a summary of the properties of object.

counts

if(type = "all")

Returns the Counts slot of object.

if(type = "biological")

Returns the Counts slot of object, biological genes only.

if(type = "technical")

Returns the Counts slot of object, tehcnical genes only.

displayTechIndicator

Returns Tech slot of object.

displaySpikeInput

Returns SpikeInput slot of object.

displayGeneNames

Returns GeneNames slot of object.

displayBatchInfo

Returns BatchInfo slot of object.

References

Vallejos, Marioni and Richardson (2015). Bayesian Analysis of Single-Cell Sequencing data.

See Also

BASiCS_Data-class

Examples

# NOT RUN {
Data = makeExampleBASiCS_Data()
show(Data)
head(counts(Data))
dim(counts(Data, type="biological"))
dim(counts(Data, type="technical"))
displayTechIndicator(Data)
displaySpikeInput(Data)
displayGeneNames(Data)
displayBatchInfo(Data)
# }