metabodecon (version 1.6.2)

dohCluster: Cluster Based Peak Alignment

Description

Helper function of align(). Should not be called directly by the user.

Rewrite of speaq::dohCluster(), compatible with the data format returned by 'generate_lorentz_curves()' and 'gen_feat_mat()'. The function name "dohCluster" comes from "Do Hierarchical Clustering" which is part of the Alignment algorithm proposed by Vu et al. (2011) in doi:10.1186/1471-2105-12-405.

Direct usage of this function has been deprecated with metabodecon version 1.4.3 and will be removed with metabodecon version 2.0.0.

Usage

dohCluster(
  X,
  peakList,
  refInd = 0,
  maxShift = 100,
  acceptLostPeak = TRUE,
  verbose = TRUE
)

Value

A list containing two data frames Y and new_peakList. The first one contains the aligned spectra, the second one contains the aligned signals of each spectrum.

Arguments

X

Dataframe of signal intensities from all spectra as returned by gen_feat_mat().

peakList

List of peak indices as returned gen_feat_mat().

refInd

Number of the reference spectrum i.e. the spectrum to which all signals will be aligned to.

maxShift

Maximum number of points a value can be moved.

acceptLostPeak

Whether to allow the the alignment algorithm to ignore peaks that cannot easily be aligned with the reference spectrum.

verbose

Whether to print additional information during the alignment process.

Author

2021-2024 Wolfram Gronwald: initial version.
2024-2025 Tobias Schmidt: refactored initial version.

Examples

deps <- c("MassSpecWavelet", "impute")
deps_installed <- sapply(deps, requireNamespace, quietly = TRUE)
if (all(deps_installed)) {
    # 'speaq' requires 'MassSpecWavelet' and 'impute' to be installed
    sim_subset <- metabodecon_file("bruker/sim_subset")
    decons <- generate_lorentz_curves_sim(sim_subset)
    feat <- gen_feat_mat(decons)
    refObj <- speaq::findRef(feat$peakList)
    hclObj <- dohCluster(
        X = feat$data_matrix,
        peakList = feat$peakList,
        refInd = refObj$refInd,
        maxShift = 100,
        acceptLostPeak = TRUE,
        verbose = TRUE
    )
    str(hclObj, 1)
}