InSilicoSpectro::InSilico::MSMSOutput 1.3.11

InSilicoSpectro::InSilico::MSMSOutput is an object implementing common display/output methods for masses.

ATTRIBUTES

spectrum

A reference to a hash such as computed by MassCalculator::getFragmentMasses or an object of class MSMSTheoSpectrum.

expSpectrum

A reference to an experimental spectrum such as required by MassCalculator::matchClosest or an object of class ExpSpectrum. When this parameter is specified the constructor will assume that the hash spectrum contains data about the match with this experimental spectrum.

massIndex

The mass index in the experimental peak vectors, default 0. If expSpectrum parameter is an ExpSpectrum object this index is read from the object directly.

intensityIndex

The intensity index in the experimental peak vectors, default 1. If expSpectrum parameter is an ExpSpectrum object this index is read from the object directly.

tol

Relative mass error tolerance; this parameter is optional. When not specified, the matched masses found by the match algorithm are all preserved. When specified, the new tolerance is applied.

This parameter is mainly useful for match obtained via matchSpectrumClosest that does not apply any mass tolerance.

minTol

Absolute mass error, default value 0.2 Da. This parameter is used only in case tol parameter is specified, see above.

intSel

This parameter controls how the peak intensities are normalized, see function normalizeIntensities.

Parameter intSel is used provided expSpectrum was set.

prec

The number of digits after the decimal points for the masses. Default precision is 3 digits.

modifLvl

Controls how the modifications are highlighted in the vector splitPept defined below, see also function annotatePept.

cmp

This parameter is a reference to a comparison function used for sorting fragment names. If cmp is not set, the function cmpFragTypes is used instead.

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Requirements:

· Perl