ume1.5.2 package

Add metainformation derived from ume::known_mf

Add Missing Isotope Columns to mfd

Check format of peaklist

Molecular Formula Assignment

Create a Data Summary Table for Element Ratios and Parameters

Calculate Double Bond Equivalent (DBE)

Calculate UME Evaluation Parameters

Calculate Exact Monoisotopic Mass of a Molecule

Calculate Degradation Index (Ideg)

Calculate terrestrial indeces Iterr and Iterr2 (after Medeiros et al. ...

Calculate absolute mass accuracy range (ma)

Calculate mass accuracy

Calculate neutral molecular mass

Calculate Nominal Mass of a Molecule

Calculate Normalized Peak Intensities

Calculate Number of Molecular Formula Assignments per Peak

Calculate number of molecular formulas that were assigned to a molecul...

Calculate Pielou's Evenness

Recalibrate mass spectra

Calculate the Shannon Diversity Index

Calculate the Simpson Diversity Index

Check format of formula library

Check format of molecular formula data

Check data.table structure

Classify FTMS files into categories based on filename patterns

Create a Custom Interpolated Color Palette

Convert Data Table with Element Counts to Molecular Formulas

Convert Molecular Formulas to a Data Table of Element Counts

Create a custom molecular formula library for UltraMassExplorer

Create a molecular formula library for UME

Convert numeric m/z vector into minimal peaklist

Extract UME library version from formula library object

Internal helper: pretty label lookup

Apply basic filters to peaklist

Load a peaklist from file

Conditional message output for verbose functions

CENTRAL PALETTE REGISTRY

Ensure required peaklist columns are present

Data table schemas used in ume

Download and Load a UME Formula Library from Zenodo

Evaluate isotope information

Export UME Analysis Results

Extract Acquisition Parameters from All PDF Files in a Folder

Extract Acquisition Parameters from a Bruker PDF Report

Extract Metadata from UFZ FTMS Filenames

Create Customized Color Scales

Retrieve a Palette and a Representative Default Color

Filter by (relative) peak magnitude

Automated filter for mass accuracy

Filter molecular formula data by mass spectrometric metadata

Retrieve NIST element and isotope data

Check whether an object is a UME peaklist

load_ume_results

Common parameters for ume package functions

Order columns

Read xml peaklists generates ultrahigh-resolution MS analyses

Remove molecular formulas detected in blanks

Remove empty columns

Remove columns that contain ID's

Remove columns that only have one specific value

Revert data.table column names

Subsetting known molecular formula categories

theme_uplots

Complete formula assignment (wrapper function)

Complete Formula subsetting / filtering (wrapper)

uplot_cluster

Plot of Molecular Mass (M) vs. Number of Carbon Atoms (C)

Frequency Plot of DBE - O

Plot DBE vs Carbon Atoms

Plot DBE vs Oxygen Atoms (cf. Herzsprung et al. 2014) with Option for ...

Plot DBE vs ppm with Option for Interactive Plot

Histogram of Mass Accuracy

Mass Accuracy Frequency Histogram

Frequency Plot of a Selected Variable

H/C vs Molecular Mass Plot

Heteroatom Combination vs Mass Accuracy

Precision of Isotope Abundance

Kendrick Mass Defect (KMD) vs. Nominal Mass Plot

Internal: Apply UME layout styling to plotly figures

Plot LC-MS Spectrum (or fallback MS if no RT available)

Plot Mass Accuracy vs m/z

Plot Mass Spectrum

Number of Molecular Formulas per Sample Plot

uplot_pca

Plot Median of Mass Accuracy per Sample (ppm)

Molecular Formula Ratio Plot (Sample vs Control)

Check Reproducibility of Sample Analyses

Average Relative Intensity per Sample

uplot_vk

Outlier detection using multiple statistical tests

Validate UME peaklist structure