compoundQuantiles-class {CAMERA} | R Documentation

## 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, hendrik.treutler@ipb-halle.de

### See Also

`compoundQuantiles` `getAtomCount` `getIsotopeProportion`

[Package CAMERA version 1.40.0 Index]