cpArguments: Method that returns the 'arguments' slot in a 'CancerPanel'...

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

Method that returns the arguments slot in a CancerPanel object.

Description

This method returns a list with the panel general information after the creation of the object.

Usage

cpArguments(object)

Arguments

object

a CancerPanel object

Details

The length of the output list is always defined by 5 elements. For example, if there are no rs numbers present in the panel, the data.frame in dbSNP_rs element will be simply empty. The first 4 elements are filled at the very creation of the object with newCancerPanel. The tumor_type element is filled after data request with getAlterations.

Value

A list of 5 elements, one for each alteration type:

genedata	a data.frame with the cds and cds plus utr of the requested genes.
dbSNP_rs	a data.frame with all the rs number translated in genomic hg19 positions.
panel	a data.frame with the original panel information plus the length of each alteration.
drugs	a character vector containing unique drug names as reported in the panel.
tumor_type	a character vector with the tumor types requested in the panel.

Author(s)

Giorgio Melloni , Alessandro Guida

References

Source of gene length and exon structure.

See Also

cpData cpDataSubset

Examples

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

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