MinimumDistance (version 1.16.0)

MAP: Computes the maximum a posteriori trio copy number state for the segmented minimum distance

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.