sigaR (version 1.18.0)

getSegFeatures: Identical signature features selection from cghCall-object.

Description

Given an example, selects features (contiguous to the example) with the same signature (as the example) across samples from an cghCall-object.

Usage

getSegFeatures(featureNo, CNdata, verbose=TRUE)

Arguments

featureNo

Row number of example feature.

CNdata

Object of class cghCall.

verbose

Logical indicator: should intermediate output be printed on the screen?

Value

Object of class numeric, containing the row numbers of those contiguous features with the same segmented log2-ratio signatures as featureNo across samples.

References

Van Wieringen, W.N., Berkhof, J., Van de Wiel, M.A. (2010), "A random coefficients model for regional co-expression associated with DNA copy number", Statistical Applications in Genetics and Molecular Biology, Volume 9, Issue1, Article 25, 1-28.

See Also

cghCall, RCMestimation.

Examples

# load data
data(pollackCN16) 

# feature of interest
featureNo <- 7

# extract all features with identical copy number signature (over the samples)
getSegFeatures(featureNo, pollackCN16)