MAP: Computes the maximum a posteriori trio copy number state for...

In MinimumDistance: A Package for De Novo CNV Detection in Case-Parent Trios

Description

This functions is deprecated and will be defunct in a future release. The replacement function is MAP2.

Usage

MAP(
  object,
  ranges,
  id,
  TAUP = 1e+10,
  tauMAX = 1 - 5e-08,
  cnStates = c(-2, -0.4, 0, 0, 0.4, 1),
  pr.nonmendelian = 1.5e-06,
  mdThr = 0.9,
  ...
)

Arguments

object	see showMethods(MAP)
ranges	A GRanges object
id	character string for sample identifier
TAUP	scalar for transition probabilities
tauMAX	the maximum probability that the current state is the same as the previous state
cnStates	character vector for hidden Markov model state labels
pr.nonmendelian	numeric: the a priori probability of a non-Mendelian copy number alteration
mdThr	a length-one numeric vector. A minimum distance below this threshold in absolute value will not be evaluated for copy number alterations.
...	Ignored.

MinimumDistance documentation built on Nov. 8, 2020, 11:11 p.m.