annoCompoundClass: automatically annotate compound classes comments table

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

Description

automatically annotate compound classes comments table

Usage

annoCompoundClass(object, ...)

Arguments

object	a compMS2 class object.
overWrite	logical should any existing compound_class types be overwritten in the comments table (default = FALSE).
minSimScore	numeric mimimum chemical similarity score (default = 0.8), all chemical fingerprints with similarity above this score to entries of HMDB, drugBank and T3DB will be considered for the compound class. The highest chemical similarity score above this threshold will be considered as the predicted compounds class. In the event of multiple tied maximum chemical similarity scores the most frequent compound class will added to the comments table.

Details

This function attempts to automatically add chemical taxonomy information to the metID comments table accessible using Comments(object). Pre-existing compound class information can be overwritten. Additionally a predicted compound class is added for any compound not contained in HMDB, drugBank or T3DB above a minimum chemical similarity score.

Value

the compMS2 class object with compound classes (currently only phospholipids supported) contained in data(lipidAbbrev) annotated and interpreted lipid tail information added to the Comments table accessible by Comments(object).

a compMS2 class object with the compound class of the identified compound added to the metID comments table. Comments(object). Additionally a barplot is generated summarizing the identified compound class information returned.

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