fit.copy.number: Fit copy number
In Wedge-Oxford/battenberg: Battenberg subclonal copy number caller

fit.copy.number

R Documentation

Fit copy number

Description

Function that will fit a clonal copy number profile to segmented data. It first matches the raw LogR with the segmented BAF to create segmented LogR. Then ASCAT is run to obtain a clonal copy number profile. Beyond logRsegmented it produces the rho_and_psi file and the cellularity_ploidy file.

Usage

fit.copy.number(
  samplename,
  outputfile.prefix,
  inputfile.baf.segmented,
  inputfile.baf,
  inputfile.logr,
  dist_choice,
  ascat_dist_choice,
  min.ploidy = 1.6,
  max.ploidy = 4.8,
  min.rho = 0.1,
  max.rho = 1,
  min.goodness = 63,
  uninformative_BAF_threshold = 0.51,
  gamma_param = 1,
  use_preset_rho_psi = F,
  preset_rho = NA,
  preset_psi = NA,
  read_depth = 30
)

Arguments

`samplename`	Samplename used to name the segmented logr output file
`outputfile.prefix`	Prefix used for all output file names, except logRsegmented
`inputfile.baf.segmented`	Filename that points to the BAF segmented data
`inputfile.baf`	Filename that points to the raw BAF data
`inputfile.logr`	Filename that points to the raw LogR data
`dist_choice`	The distance metric that is used internally to rank clonal copy number solutions
`ascat_dist_choice`	The distance metric used to obtain an initial cellularity and ploidy estimate
`min.ploidy`	The minimum ploidy to consider (Default 1.6)
`max.ploidy`	The maximum ploidy to consider (Default 4.8)
`min.rho`	The minimum cellularity to consider (Default 0.1)
`max.rho`	The maximum cellularity to consider (Default 1.0)
`min.goodness`	The minimum goodness of fit for a solution to have to be considered (Default 63)
`uninformative_BAF_threshold`	The threshold beyond which BAF becomes uninformative (Default 0.51)
`gamma_param`	Technology parameter, compaction of Log R profiles. Expected decrease in case of deletion in diploid sample, 100 "%" aberrant cells; 1 in ideal case, 0.55 of Illumina 109K arrays (Default 1)
`use_preset_rho_psi`	Boolean whether to use user specified rho and psi values (Default F)
`preset_rho`	A user specified rho to fit a copy number profile to (Default NA)
`preset_psi`	A user specified psi to fit a copy number profile to (Default NA)
`read_depth`	Legacy parameter that is no longer used (Default 30)