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()