MAP {MinimumDistance} | R Documentation

## 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.

[Package MinimumDistance version 1.31.1 Index]