annotateVOC {ptairMS} | R Documentation

## 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)

[Package ptairMS version 1.0.1 Index]