bootstrapResults: Bootstrapping variant fits

In lima1/PureCN: Copy number calling and SNV classification using targeted short read sequencing

Bootstrapping variant fits

Description

This function bootstraps variants, then optionally re-ranks solutions by using the bootstrap estimate of the likelihood score, and then optionally removes solutions that never ranked high in any bootstrap replicate.

Usage

bootstrapResults(res, n = 500, top = NULL, reorder = FALSE)

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. If NULL, do not filter solutions.
reorder	Reorder results by bootstrap value.

Value

Returns a runAbsoluteCN object with added 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")

lima1/PureCN documentation built on Nov. 22, 2024, 6:07 a.m.