curateFAannotations | R Documentation |
after FA annotation using annotateFA, the resulting data frame can be modified to remove rows with unwanted annotation, iniRT and endRT can be changed to redefine peak limits and extra rows may be written to add new annotations. FAid should also be modified to contain unique names such as "FA(16:1)n7" and "FA(16:1)n10" instead of generic "FA(16:1)". For unknown fatty acids use FA(16:1)nx (nx, ny and nz are availables for all FA).
Internal standards can also be added to normalize data later. Leave ID and Adducts columns empty, write "IS" at the FAid column and add mz, RT, iniRT and endRT information.
curateFAannotations(msbatch, faid, dmz = 10)
msbatch |
annotated msbatch. |
faid |
data frame with 7 columns (ID, FAid, Adducts, mz, RT, iniRT and endRT) containing curated FAs. |
dmz |
mz tolerance in ppm. |
Modify FA annotations
annotated msbatch.
M Isabel Alcoriza-Balaguer <maribel_alcoriza@iislafe.es>
## Not run:
msbatch <- annotateFA(msbatch, dmz = 5)
plots <- plotFA(msbatch, dmz = 10)
pdf("FAs.pdf")
for (p in 1:length(plots)){
print(plots[[p]])
}
dev.off()
write.csv(msbatch$fas, file="faid.csv", row.names=FALSE)
faid <- read.csv("faid_curated.csv", sep=",", dec=".")
msbatch <- curateFAannotations(msbatch, faid)
## End(Not run)
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