cpData: Method that returns the 'dataFull' slot in a 'CancerPanel'...

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

Method that returns the dataFull slot in a CancerPanel object.

Description

This method returns a list with an element for each alteration type contained in the class CancerPanel slot dataFull

Usage

cpData(object)

Arguments

object

a CancerPanel object

Details

The length of the output list is always defined by 4 elements 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 NULL values. Every element is a list of 2 elements:

• data A data.frame in a format specific for the alteration type.

• Samples The second element is a list of vectors containing the names of the samples for each tumor type.

Value

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

mutations	A list of 2 elements containing the mutation alterations for each gene requested in the panel.
copynumber	A list of 2 elements containing the copynumber alterations for each gene requested in the panel.
expression	A list of 2 elements containing the expression alterations for each gene requested in the panel.
fusions	A list of 2 elements containing the fusions alterations for each gene 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

cpDataSubset

Examples

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

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