Description Usage Arguments Details Value Author(s) References See Also Examples
The 'threshold' method estimates a suitable threshold Theta from the data. Thresholding provides the ability the define distinct Loci of Enhanced Significance (LES) with the 'regions' method in a later step.
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object |
Object of class 'Les' as returned by 'estimate' or 'Les'. |
grenander |
Logical indicating whether the Grenander estimator for the cumulative density should be used (default: FALSE). For details see below and at the 'GSRI' package. |
verbose |
Logical indicating whether a summary of the estimated number of regulated probes should be printed on screen (default: FALSE). |
... |
Further arguments passed to subsequent functions. |
This method estimates the number of probes with a significant effect R. The estimation is based on the p-value distribution. The analysis is based on the 'Gene Set Regulation Index' by Bartholome et al., 2009.
Estimation of the threshold is independent of the computation performed by the 'estimate' method.
A reasonable estimate for the cutoff value Theta can be chosen such that |Lambda >= Theta| = R.
The Grenander estimator for the cumulative density results in a conservative estimate for the number of significant probes with decreased variance.
A reasonable subsequent step is to call 'regions' to find distinct Loci of Enhanced Significance.
Object of class 'Les' with additionally filled slots:
nSigProbes |
Estimated number of significant probes. |
theta |
Estimated threshold Theta. |
Julian Gehring
Maintainer: Julian Gehring <julian.gehring@fdm.uni-freiburg.de>
Kilian Bartholome, Clemens Kreutz, and Jens Timmer: Estimation of gene induction enables a relevance-based ranking of gene sets, Journal of Computational Biology: A Journal of Computational Molecular Cell Biology 16, no. 7 (July 2009): 959-967. http://www.liebertonline.com/doi/abs/10.1089/cmb.2008.0226
Package:
les-package
Class:
Les
Methods and functions:
Les
estimate
threshold
regions
ci
export
plot
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