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

Description Usage Arguments Value Author(s)

View source: R/EaCoN_functions.R

Description

This function performs the joint L2R and BAF segmentation using FACETS CBS-based bivariate segmenter, centering and calling of WES data.

Usage

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  Segment.FACETS(data = NULL, smooth.k = NULL, BAF.filter = .75, homoCut = .05,
  penalty = 100, recenter = "l2r.centeredpeak", calling.method = "mad",
  nrf = .5, SER.pen = 2, 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 FACETS (see ?facets::preProcSample() and ?facets::procSample()).

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.