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,
  ppm_formula = 30,
  top_formula = 5,
  extra_formula = TRUE,
  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,
  ppm_formula = 30,
  top_formula = 5,
  extra_formula = TRUE,
  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,
  ppm_formula = 30,
  top_formula = 5,
  extra_formula = TRUE,
  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,
  ppm_formula = 30,
  top_formula = 5,
  extra_formula = TRUE,
  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
ppm_formula	ppm tolerance of the calcMF function of the MassTools package
top_formula	maximum number of top formulas to be returned (parameters of the calcMF function of the MassTools package)
extra_formula	if TRUE, the calcMF function from MassTools package is used to calculate molecular formulas from a monoisotopic mass when no matches are found with HBDB
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 Jan. 13, 2025, 6:51 p.m.