compareSpectra-methods {MSnbase} | R Documentation

## Compare Spectra of an 'MSnExp' or 'Spectrum' instances

### Description

This method compares spectra (`Spectrum` instances) pairwise or all spectra of an experiment (`MSnExp` instances). Currently the comparison is based on the number of common peaks `fun = "common"`, the Pearson correlation `fun = "cor"`, the dot product `fun = "dotproduct"` or a user-defined function.

For `fun = "common"` the `tolerance` (default `25e-6`) can be set and the tolerance can be defined to be relative (default `relative = TRUE`) or absolute (`relative = FALSE`). To compare spectra with `fun = "cor"` and `fun = "dotproduct"`, the spectra need to be binned. The `binSize` argument (in Dalton) controls the binning precision. Please see `bin` for details.

Instead of these three predefined functions for `fun` a user-defined comparison function can be supplied. This function takes two `Spectrum` objects as the first two arguments and `...` as third argument. The function must return a single `numeric` value. See the example section.

### Methods

`signature(object1 = "MSnExp", object2 = "missing", fun = "character", ...)`

  Compares all spectra in an `MSnExp` object. The `...` arguments are passed to the internal functions. Returns a `matrix` of dimension `length(object1)` by `length(object1)`.

`signature(object1 = "Spectrum", object2 = "Spectrum", fun = "character", ...)`

  Compares two `Spectrum` objects. See the above explanation for `fun` and `...`. Returns a single `numeric` value.

### Author(s)

Sebastian Gibb <mail@sebastiangibb.de>

### References

Stein, S. E., & Scott, D. R. (1994). Optimization and testing of mass spectral library search algorithms for compound identification. Journal of the American Society for Mass Spectrometry, 5(9), 859-866. doi: https://doi.org/10.1016/1044-0305(94)87009-8

Lam, H., Deutsch, E. W., Eddes, J. S., Eng, J. K., King, N., Stein, S. E. and Aebersold, R. (2007) Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics, 7: 655-667. doi: https://doi.org/10.1002/pmic.200600625

### See Also

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

### Examples

    s1 <- new("Spectrum2", mz=1:10, intensity=1:10)
    s2 <- new("Spectrum2", mz=1:10, intensity=10:1)
    compareSpectra(s1, s2)
    compareSpectra(s1, s2, fun="cor", binSize=2)
    compareSpectra(s1, s2, fun="dotproduct")

    ## define our own (useless) comparison function (it is just a basic example)
    equalLength <- function(x, y, ...) {
      return(peaksCount(x)/(peaksCount(y)+.Machine$double.eps))
    }
    compareSpectra(s1, s2, fun=equalLength)
    compareSpectra(s1, new("Spectrum2", mz=1:5, intensity=1:5), fun=equalLength)
    compareSpectra(s1, new("Spectrum2"), fun=equalLength)

    data(itraqdata)
    compareSpectra(itraqdata[1:5], fun="cor")

[Package MSnbase version 2.10.1 Index]