This is the readme file for the dims_processing repository.
Use the hrms_promt_POS.R or hrms_prompt_NEG.R scripts to set up your working directories, and source the main script (hrms_POS.R or hrms_NEG.R).
Put these scripts and the LipidLists files in your working directory.
Note that you can make your own lipid lists using the lipid list generator excel file.
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setwd("D:/Data_processing work shop_HRMS_MAR2015") ### where your mzXML files are stored and where processed files will be saved
source("hrms_POS.R") ####directory where the hrms_POS.R script is stored (ensure LipidLists are in the working directory)
library(xcms)
library(data.table)
files = list.files(".", pattern=".mzXML")
system.time(
for (i in 1:length(files)) {
main(files[i], rtwin=c(20,60), mzwin=c(200,1200))
}
)
results <- signals_deviations()
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