bin-methods: Bin 'MSnExp' or 'Spectrum' instances

In lgatto/MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics

Bin 'MSnExp' or 'Spectrum' instances

Description

This method aggregates individual spectra (Spectrum instances) or whole experiments (MSnExp instances) into discrete bins. All intensity values which belong to the same bin are summed together.

Methods

signature(object = "MSnExp", binSize = "numeric", verbose = "logical")

Bins all spectra in an MSnExp object. Use binSize to control the size of a bin (in Dalton, default is 1). Displays a control bar if verbose set to TRUE (default). Returns a binned MSnExp instance.

signature(object = "Spectrum", binSize = "numeric", breaks = "numeric", msLevel. = "numeric")

Bin the Spectrum object. Use binSize to control the size of a bin (in Dalton, default is 1). Similar to hist you could use breaks to specify the breakpoints between m/z bins. msLevel. defines the level of the spectrum, and if msLevel(object) != msLevel., cleaning is ignored. Only relevant when called from OnDiskMSnExp and is only relevant for developers.

Returns a binned Spectrum instance.

Author(s)

Sebastian Gibb <[e-mail]>

See Also

clean, pickPeaks, smooth, removePeaks and trimMz for other spectra processing methods.

Examples

s <- new("Spectrum2", mz=1:10, intensity=1:10)
intensity(s)
intensity(bin(s, binSize=2))

data(itraqdata)
sum(peaksCount(itraqdata))
itraqdata2 <- bin(itraqdata, binSize=2)
sum(peaksCount(itraqdata2))
processingData(itraqdata2)

lgatto/MSnbase documentation built on Nov. 12, 2024, 10:58 a.m.