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]