Segment BAF with the inclusion of structural variant breakpoints - This function is now deprecated, call segment.baf.phased instead

This function takes the SV breakpoints as initial segments and runs PCF on each of those independently. The SVs must be supplied as a simple data.frame with columns chromosome and position

segment.baf.phased.sv(
  samplename,
  inputfile,
  outputfile,
  svs = NULL,
  gamma = 10,
  phasegamma = 3,
  kmin = 3,
  phasekmin = 3,
  no_segmentation = F,
  calc_seg_baf_option = 1
)

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

svs

Data.frame 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. (Default: 1)

Author

sd11