segment.baf.phased: Segment BAF, with the possible inclusion of structural...
In Wedge-lab/battenberg: Battenberg subclonal copy number caller

segment.baf.phased

R Documentation

Segment BAF, with the possible inclusion of structural variant breakpoints

Description

This function breaks the genome up into chromosomes, possibly further when SV breakpoints are provided, and runs PCF on each to segment the chromosomes independently.

Usage

segment.baf.phased(
  samplename,
  inputfile,
  outputfile,
  prior_breakpoints_file = NULL,
  gamma = 10,
  phasegamma = 3,
  kmin = 3,
  phasekmin = 3,
  no_segmentation = F,
  calc_seg_baf_option = 3
)

Arguments

`samplename`	Name of the sample, which is used to name output figures
`inputfile`	String that points to the output from the `combine.baf.files` function. This contains the phased SNPs with their BAF values
`outputfile`	String where the segmentation output will be written
`prior_breakpoints_file`	String that points to a file with prior breakpoints (from SVs for example) with chromosome and position columns (Default: NULL)
`gamma`	The gamma parameter controls the size of the penalty of starting a new segment during segmentation. It is therefore the key parameter for controlling the number of segments (Default 10)
`phasegamma`	Gamma parameter used when correcting phasing mistakes (Default 3)
`kmin`	Kmin represents the minimum number of probes/SNPs that a segment should consist of (Default 3)
`phasekmin`	Kmin parameter used when correcting phasing mistakes (Default 3)
`no_segmentation`	Do not perform segmentation. This step will switch the haplotype blocks, but then just takes the mean BAFphased as BAFsegm
`calc_seg_baf_option`	Various options to recalculate the BAF of a segment. Options are: 1 - median, 2 - mean, 3 - ifelse median==0 or 1, median, mean. (Default: 3)