findOutliers.func

0th

Percentile

Function to identify outlier clones

The function identified the clones that are outliers.

Keywords
models
Usage
findOutliers.func(thres, factor = 4, statesres)
Arguments
thres
Estimate of experimental variability, generally, madGenome
factor
Factor indicating how many standard
statesres
The states output of the hmm.run.func
Details

The outliers are the clones that are dissimilar enough from the clones assigned to the same state. Magnitude of the factor determines how many MADs away from a median a value needs to be to be declared an outlier. Outliers consitent over many samples may indicate technological artificat with that clone or possibly copy number polymorpism.

Value

outlier
Binary matrix with a row for each clone and column for each sample. "1" indicates outlier, 0 otherwise.
pred.obs.out
Matrix with a row for each clone and column for each sample. The entries are the median value for the state with outliers exceluded for all clones but outliers. The value if the observed value for the outliers.
pred.out
Matrix with a row for each clone and column for each sample. The entries are the median value for the state

References

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

See Also

aCGH

Aliases
  • findOutliers.func
Documentation reproduced from package aCGH, version 1.50.0, License: GPL-2

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