randomRecurrence: panConusig::randomRecurrence

In UCL-Research-Department-of-Pathology/panConusig: Pan-cancer copy number signatures analysis

panConusig::randomRecurrence

Description

Randomly samples new copy number profiles based on those provided. Segment boundaries for whole chromosomes are drawn from the samples provided in ascat. Signature assignemnts are sampled from all signature assignments in ascat for which the segment length class matched that of the segment being drawn for. Recurrence of the signature is then calculated across all samples from a given replicate.

Usage

randomRecurrence(ascat,
                            windowGR,
                            nrep,
                            nsim)

Arguments

ascat	Copy number profiles from which to simulate new datasets. Must include copy number signature assignment to segments. See runAssignment().
windowGR	Windows in which to calculate recurrence of randomly generated datasets. See setupWindows(). Should match those used for getRecurrence().
nrep	Number of replicates to run (number of random datasets to generate).
nsim	Number of samples to simulate per random dataset.
whichsig	Which signature to return values for.

Value

Matrix of recurrence of a given copy number signature (whichsig) across nrep simulations in genomic windows.

UCL-Research-Department-of-Pathology/panConusig documentation built on March 25, 2022, 12:18 a.m.