Segment BAF, with the possible inclusion of structural variant breakpoints — segment.baf.phased.multisample • Battenberg

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.

segment.baf.phased.multisample(
  samplename,
  inputfile,
  outputfile,
  prior_breakpoints_file = NULL,
  gamma = 10,
  calc_seg_baf_option = 3,
  GENOMEBUILD
)

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)
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)
GENOMEBUILD: Genome build upon which the 1000G SNP coordinates were obtained

Author

jdemeul, sd11