BASiCS (version 0.7.30)

BASiCS_D_Data-methods: S4 methods for BASiCS_D_Data objects

Description

S4 methods for BASiCS_D_Data-class objects.

Usage

# S4 method for BASiCS_D_Data
show(object)
# S4 method for BASiCS_D_Data
counts(object, type = "all", samples = "test")
# S4 method for BASiCS_D_Data
displaySpikeInput(object, samples = "test")
# S4 method for BASiCS_D_Data
displayTechIndicator(object)

Arguments

object

A BASiCS_D_Data object.

type

Only required for counts method. A string indicating which genes must be returned. Valid values: "all", "biological" and "technical"

samples

A string indicating which samples must be returned. Valid values: "test" and "reference".

Value

show

Prints a summary of the properties of object.

counts

if(type = "all")

Returns the CountsTest or CountsRef slot of object (depending on the value of sample).

if(type = "biological")

Returns the CountsTest or CountsRef slot of object (depending on the value of sample), biological genes only.

if(type = "technical")

Returns the CountsTest or CountsRef slot of object (depending on the value of sample), tehcnical genes only.

if(samples == "test")

Returns counts in the test sample.

if(samples == "reference")

Returns counts in the reference sample.

displayTechIndicator

Returns Tech slot of object.

displaySpikeInput

if(samples == "test")

Returns SpikeInputTest slot of object.

if(samples == "reference")

Returns SpikeInputRef slot of object.

See Also

BASiCS_D_Data-class

Examples

# NOT RUN {
Data = makeExampleBASiCS_D_Data()
show(Data)
head(counts(Data, samples = "test"))
dim(counts(Data, type="biological", samples = "test"))
dim(counts(Data, type="technical", samples = "reference"))
displayTechIndicator(Data)
displaySpikeInput(Data, samples = "test")

# }