metID.CFM: Wrapper function for Competitive Fragmentation modelling...

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

Description

The function will automatically run as a parallel computation is the compMS2 object was created in parallel.

Usage

metID.CFM(object, ...)

Arguments

object	a "compMS2" class object.
featureSubSet	character vector of composite spectra names (e.g. CC_1, CC_2 etc.) otherwise the default is to perform CFM fragmentation on all composite spectra.
keepTempFiles	logical default = FALSE fraggraph-gen .csv output file will be created as temporary files otherwise if TRUE file will be retained in subdirectories named by composite spectrum name.
minPropTicEx	numeric minimum mean total ion current explained (default = 0.9) the candidate with the highest proportion of the total ion current explained above this minimum will be automatically added to the Comments table. The argument autoPossId must also be set to TRUE.
autoPossId	logical if TRUE the function will automatically add the name of the top annotation based on mean total ion current explained and metFrag score (default = FALSE). Caution if TRUE this will overwrite any existing possible_identities in the "metID comments" table. This functionality is intended as an automatic annotation identification tool prior to thorough examination of the data in compMS2Explorer. The intention is that automatic annotations can be used in the metID.rtPred retention prediction function as part of a seamless first-pass workflow.
possContam	numeric how many times does a possible annotation have to appear in the automatically generated possible annotations for it to be considered a contaminant and therefore not added to the "metID comment" table (default = 3, i.e. if a database name appears more than 3 times in the automatic annotation table it will be removed).
verbose	logical if TRUE display progress bars.

Source

1. Allen F, Pon A, Wilson M, Greiner R, and Wishart D. CFM-ID: a web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra. Nucleic Acids Res. June 2014. http://nar.oxfordjournals.org/content/early/2014/06/03/nar.gku436.full.

2. fraggraph-gen.exe file in extdata downloaded (2016/07/09, cfm-id-2.2_win32.zip) from https://sourceforge.net/p/cfm-id/wiki/Home/.

3. lpsolve.dll in extdata downloaded (2016/07/09, lp_solve_5.5.2.3_IDE_Setup.exe) from https://sourceforge.net/projects/lpsolve/.

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