metID.dbProb: selects best annotations based on substructure annotations...

In WMBEdmands/CompMS2miner: an automatable metabolite identification, visualization and data-sharing R package for high-resolution LC-MS datasets

Description

Most probable database annotations either automatically decided based on substructure type detected by the subStructure.Annotate or user supplied most probable annotations one composite spectrum at a time. Additionally any substructure either neutral loss or product ion with an available SMILES code will be matched against all of the available annotations. The function utilizes the cmp.similarity function set to mode 2 (using the size of the descriptor intersection over the size of the smaller descriptor, to deal with compounds that vary alot in size) of the ChemmineR package to calculate the similarity of the substructure to the annotated structure. The average score between 0-1 of all of the substructures annotated by the subStructure.Annotate function is returned in a new column in the "Best Annotations" panel in the compMS2Explorer and the annotations ranked accordingly. Additionally, if either a database annotation corresponds to a substructure type annotated (e.g. glucuronide) or is the name of the database entry contains the substructure name (case-insensitive) then this will be give a maximum top score of 1.

Usage

metID.dbProb(object, ...)

Arguments

object	a compMS2 class object
nameFeat	character of a unique name of a single composite spectra of interest. If not supplied (default) all most probable annotations are decided automatically and for all composite spectra. Previous most probable annotations will not be overwritten if the function is run more than once.
DBids	unique database identifier for a specific composite spectrum, in combination with nameFeat argument.
minTimesId	numeric (default = 2) the minimum number of times a particular substructure type must be identified for it to be considered. This helps to limit consideration of neutral losses/fragments that have been identified once for example by chance.
verbose	logical if TRUE display progress bars.

Value

a compMS2 class object with most probable annotation(s)

See Also

subStructure.Annotate, metID.dbAnnotate, cmp.similarity.

Examples

compMS2Example <- metID(compMS2Example, 'dbProb')

WMBEdmands/CompMS2miner documentation built on May 9, 2019, 10:02 p.m.