findOutliers.func {aCGH}R Documentation

Function to identify outlier clones

Description

The function identified the clones that are outliers.

Usage

findOutliers.func(thres = madGenome, factor = 4, statesres = states.bic)

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

Author(s)

Jane Fridlyand

References

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

See Also

aCGH


[Package aCGH version 1.1.4 Index]