runMatch: # Run matching and get annotations in a single ionization...

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

Description

The 'matchWeiz' multi-modular search method is applied to match an input of biologically derived sample data to the given MS library. Retention time (RT) correction is first applied to the input peak list using a group of peak lists of predefined mixes of chemical standards (see stdMix data description). Several constant variables are used except the input arguments, including exact mass values for possible adducts and the peak search parameter GROUP_TH which sets the minimum number of matches required to annotate a group of features. These constants can be viewed and edited by loading the data object: data("mmSettings"). The output of the function is an R object containing all annotation data, which then needs to be converted to a readable text format using the function summarizeMWresults. Please note that two MS channels (low/high) need to be available in the peak lists as data columns named with the suffix '01' and '02', respectively (e.g.: 'IL_140816_6701' and 'IL_140816_6702' would describe data of the same biological sample, but originating from channels Ms1 and Ms2).

Usage

runMatch(cameraPeaklist, rtCorrFiles, polarity, project, MSlib, massTol = 20)

Arguments

cameraPeaklist	Path to a tab delimited peak list file, as generated by the CAMERA package.
rtCorrFiles	Path to a directory containing peak list files corresponding with a predefined mix of chemical standards (see below).
polarity	The MS ionization mode (either "negative" or "positive") .
project	Any descriptive name for the current search run.
MSlib	MS library R object as generated by the buildMSlibrary function.
massTol	The mass tolarance for mass-to-mass matches, in ppm (default is 20 ppm)

Value

NULL on a succesful completion.

Examples

data(sampleLib)
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) 

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