cpArguments {PrecisionTrialDrawer} | R Documentation

## 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) )

[Package PrecisionTrialDrawer version 1.3.1 Index]