optimCutOff: optimum cutoff for a correlation or spectral similarity...

Description Usage Arguments Value References

Description

optimum cutoff for a correlation or spectral similarity matrix

Usage

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optimCutOff(x = NULL, cutOffSeq = seq(0.01, 1, 0.01), diffConsecVals = 1.5
  * 10^-3, maxCutOff = 0.95)

Arguments

x

matrix of correlation coefficients or spectral similarity values column and row names must match

cutOffSeq

numeric a vector of cut-off values to test. (default=seq(0.01, 1, 0.01) a numeric vector of length 100)

diffConsecVals

numeric the scaled difference between consecutive values to identify the plateau in the network density (default=1.5*10^-3 or 0.0015).

Value

a list containing two named elements "estCutOff" a numeric estimated optimal cut-off value and "testData" a matrix of the test results at each cut-off value. The function also plots the result.

References

Koh Aoki, Yoshiyuki Ogata, and Daisuke Shibata Approaches for Extracting Practical Information from Gene Co-expression Networks in Plant Biology Plant Cell Physiol (2007) 48 (3): 381-390 first published online January 23, 2007 doi:10.1093/pcp/pcm013


WMBEdmands/compMS2Miner documentation built on May 9, 2019, 10:04 p.m.