## TO DO ITEMS for ramclustR/csu.pmf.tools
## correct overloaded peaks for saturation correction
library(CorrectOverloadedPeaks)
CorrectOverloadedPeaks::read.mzXML()
## functionalize sirius call
# sirius -i=R:\RSTOR-PMF\Projects\20201130-ABARA-MS-994\Apple\TOF_PH_pos\spectra\ms -o=R:\RSTOR-PMF\Projects\20201130-ABARA-MS-994\Apple\TOF_PH_pos\spectra\ms\out2 --recompute --naming-convention=%compoundname formula -d bio --compound-timeout 30 -p qtof zodiac structure canopus
## functionalize MSFinder spectrum search call
# MsfinderConsoleApp mssearch -i R:\RSTOR-PMF\Projects\20201130-ABARA-MS-994\Apple\TOF_PH_pos\spectra\mat\ -o R:\RSTOR-PMF\Projects\20201130-ABARA-MS-994\Apple\TOF_PH_pos\spectra\mat\out -m MSFINDER.INI
# best to store .INI file internally and write temp file each time?
## test one file which should return 5 spectra above 0.5, 9 above 0.4
msfinder.dir <- "C:/MSFinder/msfinder"
in.dir <- "R:/RSTOR-PMF/Projects/20201130-ABARA-MS-994/test/mat/"
out.dir <- paste0(in.dir, "out/")
ini.filename <- "MSFINDER.INI"
#set the score threshold in the ini file very low - i.e. 0.05
## create path strings
msfinder <- paste0(msfinder.dir, "/", "MsfinderConsoleApp.exe")
ini <- paste0(msfinder.dir, "/", ini.filename)
## create full command for cmd prompt
cmd.string <- paste(
normalizePath(msfinder),
"mssearch -i",
normalizePath(in.dir),
"-o", normalizePath(out.dir),
"-m", normalizePath(ini)
)
## submit command to cmd
system(cmd.string)
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