dot-specSim: Calculate spectral similarity

In pmbrophy/mzDataTable: Import and convert raw mass spectrometry data formats

Description

Calculate the spectral similarity using one of the available methods. The mzDt containing n-unique seqNums is converted into a matrix with n-columns. All unique combinations are calculated and returned. The output can be further processed to a similarity matrix using similarity2SquareMatrix(). mzDt should contain self-normalized spectra (see: .normalizeEachSpectrum_dt()). Each spectrum should contain mzGrid and mzGrid_index corresponding to the global mz grid (see: indexMasterSpectrum()).

Usage

.specSim(mzDt, similarity_method)

Arguments

mzDt	the data.table containing two or more spectra to be compared.
similarity_method	choose one: "dotProd", "specContrast", "specCor", "brayCurtis", "euclidean"

Value

returns a 3-column matrix containing the similarity score and sequence numbers

pmbrophy/mzDataTable documentation built on June 6, 2020, 7:43 a.m.