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

In gustaveroussy/EaCoN: EaCoN : Easy Copy Number !

Description

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

Usage

  ASCN.SEQUENZA(data = NULL, max.ploidy = 4, ploidy.step = .1,
  seg.min.size = 1E+06, out.dir = getwd(), force = FALSE)

Arguments

data	Data object contained in a RDS file generated with Segment.SEQUENZA() (or corresponding wrappers Segment.ff() and Segment.ff.Batch(), using the "FACETS" segmenter.
max.ploidy	Maximal median ploidy value to evaluate.
ploidy.step	Step for the ploidy value to evaluate in loop.
seg.min.size	Minimal size (in nt) of a segment to be used in the model fit.
out.dir	Output directory.
force	If some result files already exist, delete them before runing.

Value

Several RDS objects, PNG plots, CBS files and data tables.

Author(s)

Bastien Job

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