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 qquantile. 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 qquantile. 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,compoundQuantilesmethod

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, hendrik.treutler@ipbhalle.de
See Also
compoundQuantiles
getAtomCount
getIsotopeProportion
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