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

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

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

CAMERA documentation built on Nov. 8, 2020, 4:59 p.m.