update.metaboSet: Update ids in a metaboSet object

In kroemerlab/GRMeta: Processing MetX data

Description

Update sample or analyte ids in an experiment object

Usage

## S3 method for class 'metaboSet'
update(obj,what="Sid",formerid=NULL,newid=NULL,exact=TRUE,swap=FALSE)

Arguments

obj	Metaboset object
what	Only Sid or Analyte supported
formerid	Vector of current Sids
newid	Vector of new Sids
exact	Exact matching
swap	Should names in oldname be swaped with corresponding newname

Value

metaboSet object

Author(s)

David Enot [e-mail]

Examples

testfiles=list.files(system.file( package = "GRMeta"),pattern = "txt$",full.names = TRUE)
mydata=loadAgilentData(ifile =testfiles[1])
print(mydata$Sid)

### Exact=TRUE: simple renaming of the Sid
mydata2=update(mydata,what="Sid",formerid=c("Bl_prerun-eau_1b","Bl_prerun-matrice_4"),newid = c("Bl-pre","BlM-pre"),exact=TRUE,swap = FALSE)
print(mydata2$File)

### Exact=FALSE: replace patterns by the second one
mydata2=update(mydata,what="Sid",formerid=c("pre","eau"),newid = c("*****",""),exact=FALSE,swap = FALSE)
print(mydata2$Meta)

### Swap two entries does ONLY exchange ids but not the file/date etc...
print(mydata$File)
mydata2=update(mydata,what="Sid",formerid="Bl_prerun-eau_1b",newid = "Bl_prerun-matrice_4",swap = TRUE)
print(mydata2$File)

############# With Analyte: exclude the method name from the analyte id
testfiles=list.files(system.file( package = "GRMeta"),pattern = "txt$",full.names = TRUE)
mydata=loadAgilentData(ifile =testfiles[1])
mydata$Analyte
mydata2=update(mydata,what="Analyte",formerid="-myassay",newid = "",exact=FALSE)
mydata2$Analyte

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