ASCN.ASCAT: Allele-Specific Copy Number estimation using ASCAT

In gustaveroussy/EaCoN: EaCoN : Easy Copy Number !

Description

This function performs the estimation of allele-specific copy number using ASCAT.

Usage

  ASCN.ASCAT(data = NULL, gammaRange = c(.35,.95), nsubthread = 1,
  cluster.type = "PSOCK", out.dir = getwd(), force = FALSE, ...)

Arguments

data	Data object contained in a RDS file generated with Segment.ASCAT() (or corresponding wrappers Segment.ASCAT.ff() and Segment.ASCAT.ff.Batch().
gammaRange	The range of gamma values to assess the modelling of ASCN (see ?ASCAT::ascat.runAscat).
nsubthread	Number of subthreads for multithreading.
cluster.type	Type of subthreading cluster (see ?parallel::makeCluster()).
out.dir	Output directory.
force	If some result files already exist, delete them before runing.
...	Any additional parameter to give to ASCAT::ascat.runAscat().

Details

Please note that depending on noise and complexity of the L2R and BAF profiles, ASCAT will not always be able to perform ASCN.

Value

Several RDS objects, PNG plots, CBS files and data tables in several folders containing the different ASCN (allele-specific copy number) analyses performed for each value in gammaRange. The optimal fit among the generated ones will be output in a separate text file.

Author(s)

Bastien Job

gustaveroussy/EaCoN documentation built on Oct. 20, 2021, 2:41 a.m.