falsePosIdentify: Identify and/or remove false positives from metID comments...

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

Description

Identify and/or remove false positives from metID comments table based on a prohibited keyword search

Usage

falsePosIdentify(object, ...)

Arguments

object	a "compMS2" class object.
prohibKeyWords	character a regular expression of prohibited keywords. If any of these are discovered in any of the abstracts returned from the PubMed Entrez search then they will be removed from the metID comments table.
n	integer number of pubmedids to return per metID comments possible_identity. (default = 50). Larger numbers may improve accuracy but increase computation time. The maximum allowed value is 500 (limited by entrez system).
meanFreqPerAbs	numeric minimum mean frequency of the summed frequencies of the prohibited keywords. Default = 0.6 that is a mean summed frequency of any of the key words in the regular expression of 0.6 for it to be considered. This limits the accidental removals of a true positive which has a low word count frequency by chance.
removeFP	logical if TRUE remove possible false positive annotations from the possible_identity column of the metID comments table. If FALSE (default) the possible false positive annotation names will remain but they will be flagged in the user_comments column of the metID comments table as "possible false positive (falsePosRemoval)".
maxChar	numeric maximum number of characters in cleaned abstract words to return.
verbose	logical if TRUE display progress bars.

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