metID.compMS2toMsp: msp file from compMS2 class object

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

Description

msp file from compMS2 class object

Usage

metID.compMS2toMsp(object, studyName = NULL, existingMsp = NULL,
  outputDir = getwd(), onlyCommented = FALSE, ...)

Arguments

object	a "compMS2" class object
studyName	character a study name tag for your dataset.
existingMsp	character a full path or web address of an existing msp database file to concatenate to. The new entries will appear underneath the last entry of the existing msp datafile file. If this argument is supplied then this file will be overwritten.
outputDir	character full path to a directory to write the msp file to. Default is to take the current working directory obtained from getwd.
onlyCommented	logical (default = FALSE) should only metabolites recorded in the comments table be included or if true all of the composite spectra.

Details

this function converts a compMS2 class object to an msp database file inserting experimental details and taking annotation data from the comments table and best annotations. This creates a means to database successive experiments and potentially concatenate to a laboratories existing spectral database. In this way previously annotated spectra from other experiments can be matched to new datasets. A unique splash code is also generated for each composite spectrum and added to each database entry in the msp file. install splash R from GitHub using devtools: devtools::install_github("berlinguyinca/spectra-hash", subdir="splashR")

Value

the msp file will be written to a file tagged with the study name and date in the output directory.

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