MassCsvFileConn-class {biodb} | R Documentation

## Mass CSV File connector class.

### Description

This is the connector class for a MASS CSV file database.

### Methods

`addPrecursorFormulae(formulae)`

  :

  Adds new formulae to the list of formulae used to recognize precursors.

  formulae: A character vector containing formulae.

  Returned value: None.

`getChromCol(ids = NULL)`

  :

  Gets a list of chromatographic columns contained in this database.

  ids: A character vector of entry identifiers (i.e.: accession numbers). Used to restrict the set of entries on which to run the algorithm.

  Returned value : A data.frame with two columns, one for the ID 'id' and another one for the title 'title'.

`getNbPeaks(mode = NULL, ids = NULL)`

  :

  Gets the number of peaks contained in the database.

  mode: The MS mode. Set it to either 'neg' or 'pos' to limit the counting to one mode.

  ids: A character vector of entry identifiers (i.e.: accession numbers). Used to restrict the set of entries on which to run the algorithm.

  Returned value: The number of peaks, as an integer.

`getPrecursorFormulae()`

  :

  Gets the list of formulae used to recognize precursors.

  Returned value: A character vector containing chemical formulae.

`isAPrecursorFormula(formula)`

  :

  Tests if a formula is a precursor formula.

  formula: A chemical formula, as a character value.

  Returned value: TRUE if the submitted formula is considered a precursor.

`setPrecursorFormulae(formulae)`

  :

  Sets the list precursor formulae.

  formulae: A character vector containing formulae.

  Returned value: None.

### See Also

Super class `CsvFileConn` and interfaces `BiodbMassdbConn`, `BiodbWritable` and `BiodbEditable`.

### Examples

    # Create an instance with default settings:
    mybiodb <- biodb::newInst()

    # Get path to LCMS database example file
    lcmsdb <- system.file("extdata",
                          "massbank_extract_lcms_2.tsv", package="biodb")

    # Create a connector
    conn <- mybiodb$getFactory()$createConn('mass.csv.file', url=lcmsdb)

    # Get an entry
    e <- conn$getEntry('PR010001')

    # Terminate instance.
    mybiodb$terminate()

[Package biodb version 1.0.4 Index]