summarizeMWresults: Summarizes 'runMatch' annotation results

In AsaphA/matchWeiz: MS reference library creation supporting multi-modular compound annotation

Description

Summarizes the annotation data files generated by runMatch. Writes either one (single MS mode) or two (coupled MS ionization modes) tab delimited text files containing a summary of the annotation hits and sorted by the annotation scores.

Usage

summarizeMWresults(project, MSlib, polarity, otherMSlib = NULL)

Arguments

project	The exact name as used for the relevant search run.
MSlib	MS library object as generated by the buildMSlibrary function.
polarity	The MS ionization mode ("negative", "positive" or "both") .
otherMSlib	The MSlib MS library object corresponding with the complimentary ionization mode.

Value

NULL. On succesful completion a delimited text file is written to the working directory containing details about the putative annotations, including: compound data and scores of the individual annotation modules (columns 1-12) information about the corresponding library entery (columns 14-34) peak group data (columns 36-42), sample intensity data and the annotation scores (last column).

Examples

data (sampleLib)
# Run matching and get annotations in a single ionization mode
tomPL_neg <- system.file("extdata/Tom_all_negative_2ch_xan.tsv",package="matchWeiz")
rtFiles_neg <- system.file("extdata/rt_files_neg",package="matchWeiz")
runMatch (tomPL_neg,rtFiles_neg,"negative","tom_test",MSlib.neg)
summarizeMWresults ("tom_test",MSlib.neg,"negative")
# Run matching and get annotations using data from both ionization mode
tomPL_pos <- system.file("extdata/Tom_all_positive_2ch_xan.tsv",package="matchWeiz")
rtFiles_pos <- system.file("extdata/rt_files_pos",package="matchWeiz")
runMatch (tomPL_pos,rtFiles_pos,"positive","tom_test",MSlib.pos)
summarizeMWresults ("tom_test",MSlib.neg,"both",MSlib.pos)

# Running time: the example annotation run using the demo library (total 76 enteries) 
# took 65 seconds (on an eight core Intel i7-3820 CPU @ 3.60GHz, 16Gb RAM) 
# Annotation versus the complete WEIZMASS library (total 3309 enteries) 
# took 341 seconds using the same hardware.

AsaphA/matchWeiz documentation built on May 5, 2019, 8:12 a.m.