annotateVOC {ptairMS} | R Documentation |
Putatively annotate VOC mz by using the reference compilation from the literature, and porpose an isotope detetcion.
annotateVOC( x, ionMassColname = "ion_mass", ppm = 20, prefix = "vocDB_", fields = c("ion_mass", "ion_formula", "formula", "mass_monoiso", "name_iupac", "pubchem_cid", "inchi", "inchikey", "ref_year", "ref_pmid", "disease_name", "disease_meshid")[c(1, 2, 5)] ) ## S4 method for signature 'ExpressionSet' annotateVOC( x, ionMassColname = "ion_mass", ppm = 50, prefix = "vocDB_", fields = c("ion_mass", "ion_formula", "formula", "mass_monoiso", "name_iupac", "pubchem_cid", "inchi", "inchikey", "ref_year", "ref_pmid", "disease_name", "disease_meshid")[c(1, 2, 5)] ) ## S4 method for signature 'data.frame' annotateVOC( x, ionMassColname = "ion_mass", ppm = 50, prefix = "vocDB_", fields = c("ion_mass", "ion_formula", "formula", "mass_monoiso", "name_iupac", "pubchem_cid", "inchi", "inchikey", "ref_year", "ref_pmid", "disease_name", "disease_meshid")[c(1, 2, 5)] ) ## S4 method for signature 'numeric' annotateVOC( x, ionMassColname = "", ppm = 50, prefix = "vocDB_", fields = c("ion_mass", "ion_formula", "formula", "mass_monoiso", "name_iupac", "pubchem_cid", "inchi", "inchikey", "ref_year", "ref_pmid", "disease_name", "disease_meshid")[c(1, 2, 5)] )
x |
Expression set object (resp. data.frame) (resp. numeric vector) containing the PTR-MS processed data (resp. containing a column with the ion mass values) (resp. containing the ion mass values) |
ionMassColname |
Character: column name from the fData (resp. from the data.frame) containing the ion mass values; [default: 'ion_mass']; this argument is not used when x is a numeric vector |
ppm |
Numeric: tolerance |
prefix |
Character: prefix for the new 'annotation' columns [default: 'vocDB_'] |
fields |
Characer vector: fields of the 'vocDB' database to be queried among: 'ion_mass' [default], 'ion_formula' [default], 'formula', 'mass_monoiso', 'name_iupac' [default], 'pubchem_cid', 'inchi', 'inchikey', 'ref_year', 'ref_pmid', 'disease_name', 'disease_meshid' |
Returns the data.frame with additional columns containing the vocDB informations for the matched ion_mass values as well as the detected isotopes
dirRaw <- system.file("extdata/exhaledAir", package = "ptairData") exhaledPtrset <- createPtrSet(dir=dirRaw, setName="exhaledPtrset", mzCalibRef = c(21.022, 60.0525), fracMaxTIC = 0.7, saveDir = NULL ) exhaledPtrset<-detectPeak(exhaledPtrset,mz=c(21,59,77)) exhaled.eset <-alignSamples(exhaledPtrset ,pValGreaterThres=0.05) # Expression Set exhaled.eset <- annotateVOC(exhaled.eset) head(Biobase::fData(exhaled.eset)) # Data frame exhaled_fdata.df <- Biobase::fData(exhaled.eset) exhaled_fdata.df <- annotateVOC(exhaled_fdata.df) head(exhaled_fdata.df) # Numeric ionMass.vn <- as.numeric(Biobase::featureNames(exhaled.eset)) annotated_ions.df <- annotateVOC(ionMass.vn) head(annotated_ions.df)