annotation: Putative annotation of VOC mz by using the reference...

In camilleroquencourt/ptairMS: Pre-processing PTR-TOF-MS Data

Putative annotation of VOC mz by using the reference compilation from the literature

Description

Putatively annotate VOC mz by using the reference compilation from the literature, and porpose an isotope detetcion.

Usage

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)]
)

Arguments

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'

Value

Returns the data.frame with additional columns containing the vocDB informations for the matched ion_mass values as well as the detected isotopes

Examples

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)

camilleroquencourt/ptairMS documentation built on June 9, 2024, 10:35 a.m.