Cluster Based Peak Alignment

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.

Usage

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

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.

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.

Author

Initial version from Wolfram Gronwald. Refactored by Tobias Schmidt in 2024.

Examples

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
)
#> 
#>  --------------------------------
#>  dohCluster will run with maxShift= 100
#>  If you want dohCluster to detect the optimal maxShift automatically,
#>  use dohCluster(..., maxShift = NULL, ...)
#>  --------------------------------
#> 
#>  aligning spectrum  1
#>  Median pearson correlation of aligned spectra: 0.9977171
#>  Alignment time:  2e-04  minutes
str(hclObj, 1)
#> List of 2
#>  $ Y           : num [1:2, 1:2048] 0.0122 0.0105 0.0122 0.0106 0.0122 ...
#>  $ new_peakList:List of 2