scnaTiming: estimate the initiation and arrival time for each SCNA...

In SunPathLab/Butte: BoUnds of Time Till Expansion, inferring the SCNA arrival time in the somatic evolution toward the most recent common ancestor of tumor sample(s).

estimate the initiation and arrival time for each SCNA segment given a file containing multiple SCNA segments, and a file containing SSNV data.

Description

estimate the initiation and arrival time for each SCNA segment given a file containing multiple SCNA segments, and a file containing SSNV data.

Usage

scnaTiming(
  scnaFile,
  ssnvFile,
  sn,
  outname,
  public = FALSE,
  pubOrSub = "pubOrSub",
  skipchunk = 19,
  mmut = 10,
  qmethod = "fullMLE",
  B = 100,
  purity = NA
)

Arguments

scnaFile	the SCNA segmentation file
ssnvFile	the SSNV file
sn	sample name
outname	output timing file name (including path)
public	somatic timeline is focused on public mutations (across multi-samples) or not (otherwise, clonal variants in the specific sample)
pubOrSub	the colname for column indicating if the mutation is public or not
skipchunk	segments with number of data points (probes) no more than this number will be skipped, set it to zero if not skipped
mmut	minimum number of mutations for running timing analysis
qmethod	the method for estimating q (probabilities of a randomly acquired mutation having allele state of aj/Nt)
B	number of bootstrap for calculating confidence interval
purity	the purity of the tumor sample. if not specified, the program will search in the ssnv file for the column with the header as sn"pu" (see example input)

Value

list: timing result; timing table (for visualization) and merged CNA data frame. For butte cases (non-identifiable), pi[1] is the lower bound, and pi[2] is the upper bound. piCI[1,] and piCI[2,] are the bootstrapped confidence interval for the two bounds, respectively.

SunPathLab/Butte documentation built on Sept. 19, 2023, 9:42 a.m.