AnnotationbyMonoIsotopicMass <- function(inputmassmat, dataA,
queryadductlist = c("M+H"), adduct_table, max.mz.diff = 10) {
# inputmassmat<-read.table('~/Documents/Emory/JonesLab/Projects/DOD/PAHs_list_dpj.txt',sep='\t',header=TRUE)
# d2<-unique(d1[,1])
inputmassmat <- inputmassmat[-which(duplicated(inputmassmat[,
2]) == TRUE), ]
mz_search_list <- {
}
for (m in 1:dim(inputmassmat)[1]) {
mz_search_list <- rbind(mz_search_list, get_mz_by_monoisotopicmass(monoisotopicmass = inputmassmat[m,
1], name = as.character(inputmassmat[m, 2]),
queryadductlist = c("positive")))
}
ghilic <- getVenn(dataA = dataA, name_a = "Experimental data",
name_b = "Search list", dataB = mz_search_list_1,
mz.thresh = max.mz.diff, time.thresh = NA, xMSanalyzer.outloc = outloc,
alignment.tool = NA)
mhilic <- merge(mz_search_list, ghilic$common, by.x = "mz",
by.y = "mz.data.B")
mhilic_2 <- merge(mhilic, hilic_data, by.x = "mz.data.A",
by.y = "mz")
mhilic_3 <- mhilic_2[order(mhilic_2$Name), ]
mhilic_3 <- mhilic_3[, -c(3, 8, 9)]
cnames <- colnames(mhilic_3)
cnames[1] <- "mz"
cnames[2] <- "theoretical.mz"
colnames(mhilic_3) <- as.character(cnames)
# write.table(mhilic_3,file='PAH_Hilic_pos_mode_matches.txt',sep='\t',row.names=FALSE)
return(mhilic_3)
}
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