compoundQuantiles-class: Class compoundQuantiles encapsulates compound statistics from...

In sneumann/CAMERA: Collection of annotation related methods for mass spectrometry data

Class compoundQuantiles encapsulates compound statistics from different databases.

Description

The user is able to get the expected number of atoms of element e (C, N, ...) for a compound of mass m for a q-quantile. I.e. getAtomCount(object = compoundQuantiles(), element = e, mass = m, quantile = q) returns the number of atoms of element e in a compound of mass m in the lowest-(q*100) (sorted ascending by the possible number of atoms of element e for compounds of such mass).

The user is able to get the expected proportion between the intensities of two isotope peaks for a compound of mass m for a q-quantile. I.e. getIsotopeProportion(object = compoundQuantiles(), isotope1 = i1, isotope2 = i2, mass = m, quantile = q) returns the isotope proportion i1 / i2 for a compound of mass m in the lowest-(q*100) (sorted ascending by the possible isotope proportions for compounds of such mass).

Objects from the Class

Objects can be created with the compoundQuantiles constructor.

Slots

compoundLibrary:

The compound library to rely on (kegg, chebi, ...)

massWindowSize:

The mass window size of the compound statistics (25, 100, ...)

minCompoundMass:

Minimum compound mass for which there are statistics

maxCompoundMass:

Maximum compound mass for which there are statistics

numberOfMassWindows:

Number of mass windows

numberOfIsotopes:

Number of isotopes for which there are isotope ratio quantiles

isotopeSet:

The set of isotopes for which there are isotope ratio quantiles

elementSet:

The set of elements for which there are element count statistics

quantileSet:

The set of quantiles for which there are isotope ratio statistics

eleCounters_e_q_mw:

Three dimensional array containing the element count statistics (element, quantile, mass window index)

proportions_i_q_mw:

Three dimensional array containing the isotope ratio quantiles relative to the monoisotopic peak (isotope index, quantile, mass window index)

Methods

getAtomCount

signature(object = "xsAnnotate"): returns the number of atoms of the specified element for the given quantile and mass window index

getIsotopeProportion,compoundQuantiles-method

signature(object = "xsAnnotate"): returns the isotope ratio of the specified isotope for the given quantile and mass window index relative to the monoisotopic peak

Note

No notes yet.

Author(s)

Hendrik Treutler, [e-mail]

See Also

compoundQuantiles getAtomCount getIsotopeProportion

sneumann/CAMERA documentation built on April 5, 2024, 2:33 a.m.