wmtsa package says that it isn't installed even with MALDIrppa

I installed MALDIrppa using


But have gotten to the part in my code that uses the wmtsa part of the package and now I keep getting an error:

spectra <- wavSmoothing(spectra, thresh.scale = 1)
plot(spectra[[1]], main=paste0("Smoothing"),xlim=c(760, 770))
smooth <- spectra [[1]]

Error in loadNamespace(name) : there is no package called ‘wmtsa’

  1. stop(e)

  2. value[3L]

  3. tryCatchOne(expr, names, parentenv, handlers[[1L]])

  4. tryCatchList(expr, classes, parentenv, handlers)

  5. tryCatch(loadNamespace(name), error = function(e) stop(e))

  6. getNamespace(ns)

  7. asNamespace(ns)

  8. getExportedValue(pkg, name)

  9. wmtsa::wavShrink

  10. fun(intensity(x))

  11. FUN(X[[i]], ...)

  12. lapply(x, FUN = transfIntensity, fun = function(x) wmtsa::wavShrink(x, thresh.scale = thresh.scale, ...))

  13. wavSmoothing(spectra, thresh.scale = 1)

If anybody has any ideas of how to make this work I would be very grateful.

The required dependency wmsta was culled from CRAN, and the author of MALDlrppa did not reconfigure the package to pull wmsta from the archives.

Consider an alternative package, since the archived version is likely to break in the future if it hasn't already.

Can you possibly suggest a different package that does the same thing as I'm quiet new to this?

I haven't done any mass spectrometry since the Johnson Administration, so I can only suggest doing a search for that term on rseek.org and these packages from the taskview

Mass Spectrometry

  • The MSnbase defines infrastructure for mass spectrometry-based proteomics data handling, plotting, processing and quantification.
  • The MALDIquant provides tools for quantitative analysis of MALDI-TOF mass spectrometry data, with support for baseline correction, peak detection and plotting of mass spectra.
  • The OrgMassSpecR package is for organic/biological mass spectrometry, with a focus on graphical display, quantification using stable isotope dilution, and protein hydrogen/deuterium exchange experiments.
  • The FTICRMS package provides functions for Analyzing Fourier Transform-Ion Cyclotron ed Resonance Mass Spectrometry Data.
  • The titan provides a GUI to analyze mass spectrometric data on the relative abundance of two substances from a titration series.
  • The Bioconductor packages MassSpecWavelet, PROcess, and xcms are designed for the analysis of mass spectrometry data.
  • The apLCMS package is designed for the processing of LC/MS based metabolomics data.
  • The xMSanalyzer package allows merging apLCMS sample processing results from multiple sets of parameter settings, among other features.
  • The MSPrep package is for post-processing of metabolomic data, including summarization of replicates, filtering, imputation, and normalization.
  • The metaMS package is an MS-based metabolomics data processing and compound annotation pipeline.

Thanks I will have a look at them, MALDIrppa comes under the MALDIquant code that I've found so hopefully I will find a way around it

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