In jcapelladesto/geoRge: Isotopic label tracking for untargeted metabolomics

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library(geoRge)
data(mtbls213)

## Check our metabolights repository for the mzXML files used in the example below (http://www.ebi.ac.uk/metabolights/MTBLS213)
## and place it in a directory "../MTBLS213/"
## Use XCMS package (https://bioconductor.org/packages/release/bioc/html/xcms.html) for peak picking, alignment and grouping

## Parameters such as ppm, peakwidth, mzwid, minfrac and bw are not strict. They depend on data acquisition and methodology.
## Please find the best parameters for your own data using your own experience or by trial and error

Here is the actual geoRge()ing:

s1 <- PuInc_seeker(XCMSet=mtbls213,ULtag="CELL_Glc12",Ltag="CELL_Glc13",sep.pos="f")

s2 <- basepeak_finder(PuIncR=s1,XCMSet=mtbls213,ULtag="CELL_Glc12",Ltag="CELL_Glc13",
  sep.pos="f",UL.atomM=12.0,L.atomM=13.003355,
    ppm.s=6.5,Basepeak.minInt=2000)

negative <- read.table(system.file("extdata/adducts_negative.txt", package="geoRge"),
                       header=T,stringsAsFactors=F)
db <- read.csv(system.file("extdata/ExampleDatabase.csv", package="geoRge"),
                header=T,stringsAsFactors=F,fill=T)

hits <- database_query(geoRgeR = s2, adducts = negative, db = db)

# The normal script works, but breaks without different conditions. 
# Check: overwrite mtbls213 contitions

library(xcms)
library(geoRge)
data(mtbls213)

sampclass(mtbls213) <- c(rep("CELL_Glc12_05mM_Normo", 6), rep("CELL_Glc13_05mM_Normo", 6))
s1 <- PuInc_seeker(XCMSet=mtbls213,ULtag="CELL_Glc12",Ltag="CELL_Glc13",sep.pos="f")

s2 <- basepeak_finder(PuIncR=s1,XCMSet=mtbls213,ULtag="CELL_Glc12",Ltag="CELL_Glc13",
  sep.pos="f",UL.atomM=12.0,L.atomM=13.003355,
  ppm.s=6.5,Basepeak.minInt=2000)