cpDataSubset: Method that returns the 'dataSubset' slot in a 'CancerPanel'...

In gmelloni/PrecisionTrialDrawer: A Tool to Analyze and Design NGS Based Custom Gene Panels

Method that returns the dataSubset slot in a CancerPanel object.

Description

This method returns a list with an element for each alteration type. It shows the content of the slot dataSubset in the CancerPanel object.

Usage

cpDataSubset(object)

Arguments

object

a CancerPanel object

Details

The slot showed with this getter is a list of length 4 even if no data for a certain alteration type were requested. In case no data were requested or if there are no data for a certain tumor type, the slot is filled with a NULL value. If data are present but there are no alteration for the specified tumor types the slot is filled with a 0 rows data.frame.

Value

A list of 4 elements, one for each alteration type:

mutations	a data.frame containing exactly the mutation alterations requested in the panel.
copynumber	a data.frame containing exactly the copynumber alterations requested in the panel.
expression	a data.frame containing exactly the expression alterations requested in the panel.
fusions	a data.frame containing exactly the fusions alterations requested in the panel.

Author(s)

Giorgio Melloni , Alessandro Guida

References

data origin for mutations, copynumber and expression data

data origin for fusion data

See Also

cpData

Examples

# Load example CancerPanel object
data(cpObj2)
# Show slot dataSubset
str( cpDataSubset(cpObj2) )

gmelloni/PrecisionTrialDrawer documentation built on March 4, 2023, 1:48 a.m.