metID.specSimNetwork: CompMS2 spectral similarity network generation

In WMBEdmands/compMS2Miner: an automatable metabolite identification, visualization and data-sharing R package for high-resolution LC-MS datasets

Description

generates a dot product spectral similarity network from the MS/MS fragmentation data. The resulting spectral similarity network can then be viewed in compMS2Explorer. Utilizes the graph function of the igraph package.

Usage

metID.specSimNetwork(object, ...)

Arguments

object	A "compMS2" class object.
minDotProdThresh	minimum dot product spectral similarity score. If no value is supplied the default is to estimate an optimal cut-off value based on network attributes from a series of spectral similarity cut-off values. This is based upon the relationship between the number of nodes, edges, number of clusters and the network density (i.e. n actual edges/n potential edges) at each spectral similarity cut-off value. A plot showing the result of this estimation will be generated.
binSizeMS2	numeric MS2 bin size for spectral similarity matching (default = 0.1)
minClustSize	numeric minimum number of connected nodes that is cluster size (default =3). If a cluster of nodes is less than this number then it will be removed.

Value

"compMS2" class object with an additional network graph of any peakTable features above the correlation threshold.

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.