matchmzSet: Matching m/z to a database

In kroemerlab/GRMeta: Processing MetX data

Description

Matching m/z to a database

Usage

matchmzSet(obj, Analyte = NULL, annotdb = NULL, ipdb = NULL, lIP = NULL, dppm = 20, mz2use = "MZ", mass2use = "Mass", 
annotinf2add = NULL,objinf2add = NULL, groupby =NULL, chunk = 200, collsep = ";;")

Arguments

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

Value

Data frame

Author(s)

David Enot [e-mail]

Examples

## 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)

kroemerlab/GRMeta documentation built on March 25, 2020, 11:32 a.m.