optimCutOff: optimum cutoff for a correlation or spectral similarity...
In WMBEdmands/CompMS2miner: an automatable metabolite identification, visualization and data-sharing R package for high-resolution LC-MS datasets
Description
Usage
Arguments
Value
References
Description
optimum cutoff for a correlation or spectral similarity matrix
Usage
1
2
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, 10:02 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Value References
Description
optimum cutoff for a correlation or spectral similarity matrix
Usage
1 2 | 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
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.