Segment.SEQUENZA: L2R and BAF joint segmentation using SEQUENZA.

In gustaveroussy/EaCoN: EaCoN : Easy Copy Number !

Description

This function performs the joint L2R and BAF segmentation using ASPCF segmentation from copynumber used in sequenza, centering and calling of WES data.

Usage

  Segment.SEQUENZA(data = NULL, smooth.k = NULL, BAF.filter = .75, homoCut = .05,
  penalty = 50, recenter = "l2r.centeredpeak", calling.method = "mad",
  nrf = .5, SER.pen = 40, out.dir = getwd(), return.data = FALSE,
  write.data = TRUE, plot = TRUE, force = FALSE)

Arguments

data	Data object contained in a RDS file generated with EaCoN.WES.Normalize(), as this segmenter is only compatible with HTS results.
smooth.k	The half-window size for data smoothing by winsorization. If NULL, no winsorization performed.
BAF.filter	Perform a filtering of BAF noise, keeping a fraction of heterozygous BAF markers, represented by this parameter.
homoCut	Threshold value to consider a BAF segment as homozygote.
penalty	The penalty for segmentation from SEQUENZA (see gamma parameter in ?copynumber::aspcf()).
recenter	Method to perform re-centering of the L2R profile. Can be : "l2r.mainpeak" (use the highest peak of the L2R density), "l2r.centeredpeak" (use the most-centered peak), "l2r.median" (just center to the median of the L2R distribution. Not recommended), any signed numeric (to force centering to a desired level), or NULL (do not recenter).
calling.method	Method to perform the calling of aberrations (attribution of the Loss / Normal / Gain status). Can be "mad" (build threshold based on the L2R spread noise, altered by the nrf coefficient) or "density" (automatically build thresholds based on the L2R density).
nrf	Coefficient to multiply the L2R spread noise, to build a calling threshold when calling.method is set to "mad". Not used when calling.method set to "density"
SER.pen	Penalty for the small events rescue step (a second-step segmentation of the L2R profile using PELT, to retrieve small events ignored by FACETS). Can be a positive integer, or NULL (does not perform a second-step PELT segmentation at all).
out.dir	Output directory.
return.data	Return the results.
write.data	Write the results as a RDS file.
plot	Perform plots.
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.