rie: Function to culculate the Robust Initial Enhancement (RIE)

Description Usage Arguments Value Note Author(s) References Examples

Description

Function to culculate the Robust Initial Enhancement (RIE)

Usage

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	rie(x, y, decreasing=TRUE, alpha=20.0)

Arguments

x

a vector for scores

y

a vector for labels (0:inactive, 1:active)

alpha

coefficient alpha

decreasing

TRUE if the compounds are ranked by decreasing score

Value

RIE, in the range from 0 to +Inf.

Note

Though RIE was originally calculated through a Monte Carlo simulation, this function adopts a simplified formulation proposed by Truchon et al. to reduce computational cost.

Author(s)

Hiroaki YABUUCHI

References

Sheridan RP et al. Protocols for bridging the peptide to nonpeptide gap in topological similarity searches. J. Chem. Inf. Comput. Sci. (2001) 41, 1395-1406.

Truchon et al. Evaluating Virtual Screening Methods: Good and Bad Metrics for the "Early Recognition" Problem. J. Chem. Inf. Model. (2007) 47, 488-508.

Examples

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x <- rnorm(1000)  # random scores for 1000 compounds
y <- c(rep(1,50), rep(0,950))     # activity labels for "x"
rie(x, y)

data(dud_egfr)
rie(dud_egfr$energy, dud_egfr$label, decreasing=FALSE)


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