parseSeg: Parse CN seg files

In quevedor2/WadingPool: A toolkit for shallow/low-pass whole genome sequencing analysis

Description

Parses a seg file with given chromosome-separated intervals and a discrete CN state. It will identify the number of states occupying 'state_frac' of the genome, where each interval is of at least 'min_frac' in size.

Usage

parseSeg(
  segf,
  segcol = "event",
  start = "start",
  end = "end",
  state_frac = 0.9,
  min_frac = 0.05,
  get_tt = FALSE,
  get_seg = FALSE
)

Arguments

segf	path to CN seg file
segcol	character: column name for discrete CN state
start	character: column name for interval start
end	character: column name for interval end
state_frac	numeric: minimal fraction of the genome occupied by CN states (default=0.90)
min_frac	numeric: minimum segment size in fractions (default=0.05)
get_tt	boolean: return a transition state probability matrix (in.dev)
get_seg	boolean: return the sef file parsed

Value

A one or two element list: 'state': integer number of states 'tt': transition matrix

quevedor2/WadingPool documentation built on Dec. 22, 2021, 10:59 a.m.