Description Usage Arguments Value Examples
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.
1 | summarizeMWresults(project, MSlib, polarity, otherMSlib = NULL)
|
project |
The exact name as used for the relevant search run. |
MSlib |
MS library object as generated by the |
polarity |
The MS ionization mode ("negative", "positive" or "both") . |
otherMSlib |
The MSlib MS library object corresponding with the complimentary ionization mode. |
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).
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | 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.
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