In crmclean/ms2sweeper: Finding and Retreiving Best Posible MS2 Spectra

This file was generated to process the output of mummichog to find all unique mz/rt features that have some kind of exact mass matches to kegg.

mummichogIn <- read.csv(here::here("data/faahko_post_mummichog.csv"))
uniqueMummyMasses <- mummichogIn[!duplicated(mummichogIn$Query.Mass),]

storeMatches <- list()
for(i in seq_along(uniqueMummyMasses$Query.Mass)) {
    match <- abs(mummichogOut$m.z - uniqueMummyMasses$Query.Mass[i])/
        uniqueMummyMasses$Query.Mass[i] * 10^6 < 20
    storeMatches[[i]] <- which(match)
}

featureRts <- lapply(storeMatches, function(x) {
    mummichogOut$retention_time[x]
})

storeMatches <- list()
for(i in seq_along(featureRts)) {
    storeMatches[[i]] <- cbind(mzs = uniqueMummyMasses$Query.Mass[i], rts = featureRts[[i]])
}

storeMatches <- Reduce(f = rbind, x = storeMatches)
write.table(x = storeMatches, file = here::here("data/checkMS2s.txt"), row.names = F)

crmclean/ms2sweeper documentation built on May 22, 2019, 2:44 p.m.