findAber.func: Function to determines focal aberrations

In aCGH: Classes and functions for Array Comparative Genomic Hybridization data

Description

The function identifies clones that are focal aberrations.

Usage

findAber.func(maxClones = 1, maxLen = 1000, statesres)

Arguments

maxClones	Maximum number of clones assigned to the same state which can be considered to be focal aberrations
maxLen	Maximum lengeth of the region containing clones assigned to the state so that those clones can be considered to be focal aberrations
statesres	The states output of the hmm.run.func

Details

The focal aberrations are the one or more clones assigned to the state different from the states of the surrounding clones. They may indicate copy number polymorphisms or interesting high or low focal changes.

Value

aber	Binary matrix with a row for each clone and column for each sample. 1 indicates presence of a focal aberrations, 0 lack of such.

Author(s)

Jane Fridlyand

References

"Application of Hidden Markov Models to the analysis of the array CGH data", Fridlyand et.al., JMVA, 2004

aCGH documentation built on Nov. 8, 2020, 6:58 p.m.