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README.md

Build Status

MetFragR

R package for MetFrag

Details on http://c-ruttkies.github.io/MetFrag/projects/metfragr/

Installation

Installing the package locally
  • checkout the MetFragR git repository
  • build the package (on command line):
R CMD check metfRag
R CMD build metfRag
  • install the package (in R):
install.packages("metfRag",repos=NULL,type="source")
library(metfRag)
Installing the package directly from github (in R)
library(devtools)
install_github("c-ruttkies/MetFragR/metfRag")
  • if you get an error like "ERROR: loading failed for 'i386'" on windows due to rJava issues, disable multiarch builds:
install_github("c-ruttkies/MetFragR/metfRag", args="--no-multiarch")
Example (Run MetFrag)
settingsObject<-list()
settingsObject[["DatabaseSearchRelativeMassDeviation"]]<-5.0
settingsObject[["FragmentPeakMatchAbsoluteMassDeviation"]]<-0.001
settingsObject[["FragmentPeakMatchRelativeMassDeviation"]]<-5.0
settingsObject[["MetFragDatabaseType"]]<-"PubChem"
settingsObject[["NeutralPrecursorMass"]]<-253.966126
settingsObject[["PeakList"]]<-matrix(c(
90.97445, 681,
106.94476, 274,
110.02750, 110,
115.98965, 95,
117.98540, 384,
124.93547, 613,
124.99015, 146,
125.99793, 207,
133.95592, 777,
143.98846, 478,
144.99625, 352,
146.00410, 999,
151.94641, 962,
160.96668, 387,
163.00682, 782,
172.99055, 17,
178.95724, 678,
178.97725, 391,
180.97293, 999,
196.96778, 720,
208.96780, 999,
236.96245, 999,
254.97312, 999), ncol=2, byrow=TRUE)
settingsObject[["NeutralPrecursorMolecularFormula"]]<-"C7H5Cl2FN2O3"
settingsObject[["PrecursorCompoundIDs"]]<-c("50465", "57010914", "56974741", "88419651", "23354334")
#
# pre and post-processing filter
#
# define filters to filter unconnected compounds (e.g. salts)
settingsObject[["MetFragPreProcessingCandidateFilter"]]<-c("UnconnectedCompoundFilter","IsotopeFilter")
settingsObject[["MetFragPostProcessingCandidateFilter"]]<-c("InChIKeyFilter")
#run MetFrag
scored.candidates<-run.metfrag(settingsObject)
#scored.candidates is a data.frame with scores and candidate properties
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