cfmFragGraphGen: cfm fragment graph generation from table of annotations

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

Description

cfm fragment graph generation from table of annotations

Usage

cfmFragGraphGen(bestAnnoSubRow = NULL, fragGraphGenExe = NULL,
  compSpecAll = NULL, keepTempFiles = FALSE, mode = "pos",
  frag_mzabs = 0.05)

Arguments

bestAnnoSubRow	unique compMS2@BestAnno entries (only M-H (neg mode) and M+H (pos mode) can be in silico fragmented by CFM and no SubStr_types).
fragGraphGenExe	character full path to fraggraph-gen.exe file (internal to compMS2Miner package).
compSpecAll	data.frame 3 columns mass, intensity and comp spectrum index number.
mode	character ionization polarity (either 'pos' or 'neg').
frag_mzabs	numeric delta predicted-observed fragment mass accuracy for matching.

Value

if fraggraph-gen process completed then a list of fragments matched to corresponding composite spectra are return

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