FAMetA (version 0.1.7)

curateFAannotations: Modify FA annotations

Description

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.

Usage

curateFAannotations(msbatch, faid, dmz = 10)

Value

annotated msbatch.

Arguments

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.

Author

M Isabel Alcoriza-Balaguer <[e-mail]>

Details

Modify FA annotations

Examples

if (FALSE) {
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)
}