Description Usage Arguments Value Author(s) Examples
Matching m/z to a database
1 2 |
obj |
metaboSet or a data.frame |
Analyte |
Vector of analytes |
annotdb |
Dataframe containing the annotation infos |
ipdb |
Dataframe containing the IP definitions |
lIP |
List of IP, either from the Id, Name or Set columns |
dppm |
Delta ppm |
mz2use |
name of the column indicative of the m/z from the obj$Annot |
mass2use |
name of the column indicative of the mass in the annotdb |
annotinf2add |
column names in the annotdb that are added |
objinf2add |
column names in the obj$Annot that are added |
groupby |
merging lines with the same values |
chunk |
split the obj in chunks: 100-500 is OK |
collsep |
separator when merging lines |
Data frame
David Enot david.enot@gustaveroussy.fr
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 | ## Not run:
testfile=list.files(system.file( package = "GRMeta"),pattern = "roll$",full.names = TRUE)
mydata=loadMavenData(ifile =testfile[1],params = list(AssayName="prof"))
print(mydata)
## explicit use of AnnotationDB
res=matchmzSet(mydata,lIP='[M+H]1+')
## all matches in IPDB$Set='Pos1'
res0=matchmzSet(mydata,lIP='Pos1')
print(table(res$IP))
print(table(res0$IP))
## add further infos
res1=matchmzSet(mydata,lIP='[M+H]1+',annotinf2add=c('GName','MF'))
## add further infos
res2=matchmzSet(mydata,lIP='[M+H]1+',annotinf2add=c('GName','MF'),objinf2add=c('RT','MZ'))
head(res1)
head(res2)
## collapse same 'MF'
res3=matchmzSet(mydata,lIP='[M+H]1+',annotinf2add=c('GName','MF'),groupby='MF')
head(res1)
head(res3)
## collapse on Analyte: not much sense if several IPs seek for!
res4=matchmzSet(mydata,lIP='[M+H]1+',annotinf2add=c('GName','MF'),groupby='Analyte')
table(table(res2$Analyte))
table(table(res4$Analyte))
## End(Not run)
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