metabodecon (version 1.6.2)

combine_peaks: Combine Peaks

Description

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

Even after calling speaq_align(), the alignment of individual signals is not always perfect, as 'speaq' performs a segment-wise alignment i.e. groups of signals are aligned. For further improvements, partly filled neighboring columns are merged. See 'Details' for an illustrative example.

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

combine_peaks(
  shifted_mat,
  range = 5,
  lower_bound = 1,
  spectrum_data = NULL,
  data_path = NULL
)

Value

A list containing two data frames long and short. The first data frame contains one column for each data point in the original spectrum. The second data frame contains only columns where at least one entry is non-zero.

Arguments

shifted_mat

The matrix returned by speaq_align().

range

Amount of adjacent columns which are permitted to be used for improving the alignment.

lower_bound

Minimum amount of non-zero elements per column to trigger the alignment improvement.

spectrum_data

The list of deconvoluted spectra as returned by generate_lorentz_curves() that was used to generate shifted_mat. No longer required since version 1.2 of Metabodecon.

data_path

If not NULL, the returned dataframes long and short are written to data_path as "aligned_res_long.csv" and "aligned_res_short.csv".

Author

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

Details

Example of what the function does:

|            | 1    | 2    | 3    | 4    | 5    |
|----------- |------|------|------|------|------|
| Spectrum 1 | 0.13 | 0    | 0    | 0.11 | 0    |
| Spectrum 2 | 0    | 0.88 | 0    | 0.12 | 0    |
| Spectrum 3 | 0.07 | 0.56 | 0.30 | 0    | 0    |
| Spectrum 4 | 0.08 | 0    | 0.07 | 0    | 0.07 |
| Spectrum 5 | 0.04 | 0    | 0    | 0.04 | 0    |

becomes

|            | 1    | 2    | 3    | 4    | 5    |
|----------- |------|------|------|------|------|
| Spectrum 1 | 0.13 | 0    | 0    | 0.11 | 0    |
| Spectrum 2 | 0    | 0.88 | 0    | 0.12 | 0    |
| Spectrum 3 | 0.07 | 0.56 | 0    | 0.30 | 0    |
| Spectrum 4 | 0.08 | 0    | 0    | 0.07 | 0.07 |
| Spectrum 5 | 0.04 | 0    | 0    | 0.04 | 0    |

I.e.

1. Column 1 and 2 get NOT merged, because they have a common non-zero entry.

2. Column 3 and 4 get merged, because they are in range of each other and have no common non-zero entries.

3. Column 4 and 5 get NOT merged, because it is more beneficial to merge column 3 and 4, as they have more mergeable entries and after merging column 3 and 4, column 4 and 5 have a common non-zero entry.

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")
    spectrum_data <- generate_lorentz_curves_sim(sim_subset)
    shifted_mat <- speaq_align(spectrum_data = spectrum_data, verbose = FALSE)
    range <- 5
    lower_bound <- 1
    obj <- combine_peaks(shifted_mat, range, lower_bound)
    str(obj)
}