callSubclones: Fit subclonal copy number
In Wedge-lab/battenberg: Battenberg subclonal copy number caller

callSubclones

R Documentation

Fit subclonal copy number

Description

This function fits a subclonal copy number profile where a clonal profile is unlikely. It goes over each segment of a clonal copy number profile and does a simple t-test. If the test is significant it is unlikely that the data can be explained by a single copy number state. We therefore fit a second state, i.e. there are two cellular populations with each a different state: Subclonal copy number.

Usage

callSubclones(
  sample.name,
  baf.segmented.file,
  logr.file,
  rho.psi.file,
  output.file,
  output.figures.prefix,
  output.gw.figures.prefix,
  chr_names,
  masking_output_file,
  max_allowed_state = 250,
  prior_breakpoints_file = NULL,
  gamma = 1,
  segmentation.gamma = NA,
  siglevel = 0.05,
  maxdist = 0.01,
  noperms = 1000,
  seed = as.integer(Sys.time()),
  calc_seg_baf_option = 3
)

Arguments

`sample.name`	Name of the sample, used in figures
`baf.segmented.file`	String that points to a file with segmented BAF output
`logr.file`	String that points to the raw LogR file to be used in the subclonal copy number figures
`rho.psi.file`	String pointing to the rho_and_psi file generated by `fit.copy.number`
`output.file`	Filename of the file where the final copy number fit will be written to
`output.figures.prefix`	Prefix of the filenames for the chromosome specific copy number figures
`output.gw.figures.prefix`	Prefix of the filenames for the genome wide copy number figures
`chr_names`	Vector of allowed chromosome names
`masking_output_file`	Filename of where the masking details need to be written. Masking is performed to remove very high copy number state segments
`max_allowed_state`	The maximum CN state allowed (Default 100)
`prior_breakpoints_file`	A two column file with prior breakpoints, possibly from structural variants. This file must contain two columns: chromosome and position. These are used when making the figures
`gamma`	Technology specific scaling parameter for LogR (Default 1)
`segmentation.gamma`	Legacy parameter that is no longer used (Default NA)
`siglevel`	Threshold under which a p-value becomes significant. When it is significant a second copy number state will be fitted (Default 0.05)
`maxdist`	Slack in BAF space to allow a segment to be off it's optimum before becoming significant. A segment becomes significant very quickly when a breakpoint is missed, this parameter alleviates the effect (Default 0.01)
`noperms`	The number of permutations to be run when bootstrapping the confidence intervals on the copy number state of each segment (Default 1000)
`seed`	Seed to set when performing bootstrapping (Default: Current time)
`calc_seg_baf_option`	Various options to recalculate the BAF of a segment. Options are: 1 - median, 2 - mean, 3 - ifelse median==0\|1, mean, median. (Default: 3)