metisotopes

mass spectrometry utility functions and processing algorithms for analysis of stable isotope label metabolomics data.

Installation

Execute the following command in an R console:

remotes::install_github("calico/metisotopes", force=TRUE, build_vignettes=TRUE, upgrade="never")

Version Changelog

• 1.0.0 Initial public release
• 1.1.0 Major bug fixes, pipeline_diff_iso_search(), diff_iso_rescore_and_label(), diff_iso_rescore() function signature changes.

Functions

• compute_diff_scores: Computes differential isotope scores comparing control and treatment subsets.
• compute_isotopic_incorporation: Determines peak groups with isotopic incorporation by comparing early vs late time points.
• compute_time_emergent_diff_linear_model: Applies linear modeling to identify time-emergent differential abundance patterns.
• diff_iso_all_isotopes_WelchTTest: Applies Welch's T-test to compare isotopic abundances between two conditions.
• diff_iso_all_isotopes_WelchTTest_subset: Applies Welch's T-test to compare isotopic abundances with sample subsetting by regex filters.
• diff_iso_color_samples: Colors and re-orders samples based on labeled/unlabeled status.
• diff_iso_conditions_rescore_and_label: Re-scores for isotopic incorporation and tests for differential abundance by experimental conditions.
• diff_iso_emergent_significance: Tests for time-emergent differential abundance using interaction terms in linear models.
• diff_iso_m_plus_zero_fraction_WelchTTest: Identifies isotopic incorporation by comparing M+0 fractions via Welch's T-test.
• diff_iso_rescore: Re-scores peak groups based on differential isotopic abundance between sample sets.
• diff_iso_rescore_and_label: Re-scores and labels peak groups for isotopic incorporation.
• get_precomputed_iso_df: Extracts pre-computed isotopes from mzrollDB as a long-format table.
• import_isotope_mzroll: Generates a romic triple_omic object from an isotopes mzrollDB file.
• label_isotopes_by_top_hits: Labels peak groups in mzrollDB based on significant isotopic incorporation and differential abundance.
• PDB_peakgroups: Extracts the peakgroups table from an mzrollDB file.
• PDB_peaks: Extracts the peaks table from an mzrollDB file.
• PDB_sample_list: Extracts the samples table from an mzrollDB file.
• peakdetector_add_CL_argument: Adds a single command line parameter to peakdetector arguments string.
• peakdetector_add_params: Formats and adds multiple parameters to peakdetector command line.
• peakdetector_add_rt_file: Adds RT alignment file information to peakdetector command line.
• peakdetector_add_samples: Adds sample files to peakdetector command line.
• peakdetector_command_line: Generates a complete peakdetector command line for execution.
• peakdetector_default_isotope_parameters: Returns default isotope search parameters for peakdetector.
• peakdetector_default_parameters: Returns default search parameters for peakdetector.
• peakdetector_metabolite_search_params: Generates metabolomics-specific search parameters.
• pipeline_diff_iso_conditions_search: Full pipeline for differential isotope analysis with experimental design.
• pipeline_diff_iso_search: Full pipeline for differential isotope analysis between labeled and unlabeled samples.
• pipeline_time_emergent_differential_abundance: Full pipeline for time-emergent differential abundance analysis with isotopic incorporation.
• requantify_to_envelope_sum: Re-quantifies peak groups by summing isotopic envelope intensities.
• to_emergent_isotope_design_matrix: Generates design matrix for linear modeling of time-emergent isotopic incorporation.
• to_iso_matrices: Converts long-format isotope DataFrame to list of isotope matrices.
• to_M0_normalized_isotope_matrix: Normalizes isotope matrix values by dividing by M+0 isotope abundance.