bootstrapResults {PureCN} | R Documentation

## Filter unlikely purity/ploidy solutions

### Description

This function bootstraps SNVs, then re-ranks solutions by using the bootstrap estimate of the likelihood score, and then keeps only solutions that were ranked highest in any bootstrap replicate. Large-scale copy number artifacts can cause true purity/ploidy solutions rank low.

### Usage

    bootstrapResults(res, n = 500, top = 2)

### Arguments

`res` | Return object of the `runAbsoluteCN` function.
`n` | Number of bootstrap replicates.
`top` | Include solution if it appears in the top `n` solutions of any bootstrap replicate.

### Value

Returns the `runAbsoluteCN` object with low likelihood solutions removed. Also adds a bootstrap value to each solution. This value is the fraction of bootstrap replicates in which the solution ranked first.

### Author(s)

Markus Riester

### See Also

`runAbsoluteCN`

### Examples

    data(purecn.example.output)
    ret.boot <- bootstrapResults(purecn.example.output, n=100)
    plotAbs(ret.boot, type="overview")

[Package PureCN version 1.8.1 Index]