Package: mrmhub 1.0.1

Bo Burla

mrmhub: Small Molecule Mass Spectrometry Data Processing, Quality Control, and Reporting

MRMhub-QUANT, the quantitation and reporting module of the MRMhub toolchain, is a tool for processing, quality control, and visualization of targeted metabolomics and lipidomics mass spectrometry data.

Authors:Bo Burla [aut, cre], Guo Shou Teo [aut], Hyungwon Choi [aut]

mrmhub_1.0.1.tar.gz
mrmhub_1.0.1.zip(r-4.7-any)mrmhub_1.0.1.zip(r-4.6-any)mrmhub_1.0.1.zip(r-4.5-any)
mrmhub_1.0.1.tgz(r-4.6-any)mrmhub_1.0.1.tgz(r-4.5-any)
mrmhub_1.0.1.tar.gz(r-4.7-any)mrmhub_1.0.1.tar.gz(r-4.6-any)
mrmhub_1.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
mrmhub/json (API)

# Install 'mrmhub' in R:

install.packages('mrmhub', repos = c('https://slinghub.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/slinghub/mrmhub/issues

Pkgdown/docs site:https://slinghub.github.io

Datasets:

lipidomics_dataset - Plasma lipidomics dataset with metadata
quant_lcms_dataset - LC-MS dataset with external calibration curve and metadata

On CRAN:

data-processing lc-ms lipidomics mass-spectrometry metabolomics peak-identification peak-integration quality-control small-molecules

5.98 score 7 stars 41 scripts 105 exports 50 dependencies

Last updated from:46fd887f81. Checks:2 ERROR, 7 OK. Indexed: yes.

Target	Result	Time
linux-devel	ERROR	696
source / vignettes	OK	291
linux-release	OK	679
macos-release	OK	1061
macos-oldrel	OK	916
windows-devel	ERROR	855
windows-release	OK	855
windows-oldrel	OK	717
wasm-release	OK	223

Exports:add_metadata build_workflow calc_average_molweight calc_calibration_results calc_isotopic_interferences calc_qc_metrics calibrate_by_reference check_setup correct_batch_centering correct_batch_combat correct_batch_serrf correct_custom_interferences correct_drift correct_drift_cubicspline correct_drift_gam correct_drift_gaussiankernel correct_drift_loess correct_interference_manual correct_isotopic_interferences cv cv_log data_load_example data_sum_features detect_outlier_pca exclude_analyses exclude_features filter_features_qc generate_workflow_qmd get_analyis_end get_analyis_start get_analysis_breaks get_analysis_count get_analysis_duration get_analyticaldata get_batch_boundaries get_calibration_metrics get_feature_count get_featurelist get_iqr_tails get_mad_tails get_outlier_bounds get_qc_bias_variability get_response_curve_stats get_runtime_median import_data_csv_long import_data_csv_wide import_data_masshunter import_data_mrmhub import_data_mztab import_data_skyline import_metadata_analyses import_metadata_features import_metadata_from_data import_metadata_istds import_metadata_msorganiser import_metadata_qcconcentrations import_metadata_responsecurves licar_pattern_choices mrmhub_enable_cli_color mrmhub_get_plot_defaults mrmhub_reset_plot_defaults mrmhub_set_plot_defaults mrmhub_status MRMhubExperiment normalize_by_istd parse_masshunter_csv parse_mrmhub_result parse_plain_long_csv parse_plain_wide_csv parse_skyline_result plot_abundanceprofile plot_calibrationcurves plot_feature_correlations plot_interference_correction plot_matrixeffects plot_normalization_qc plot_pca plot_pca_loading plot_qc_interference_impact plot_qc_summary_byclass plot_qc_summary_overall plot_qcmetrics_comparison plot_responsecurves plot_rla_boxplot plot_rt_vs_chain plot_runscatter plot_runsequence pooled_rsd pooled_sd quantify_by_calibration quantify_by_istd read_dataset_rds save_dataset_csv save_dataset_mztab save_dataset_rds save_dataset_summarizedexperiment save_feature_qc_metrics save_metadata_msorganiser_template save_metadata_templates save_plot save_report_xlsx set_analysis_order set_intensity_var set_lipid_class summarize_interferences

Dependencies:assertr bit bit64 cli clipr cpp11 crayon dplyr farver forcats fs generics ggh4x ggnewscale ggplot2 ggrepel glue gtable hms isoband labeling lifecycle lubridate magrittr MASS openxlsx2 pillar pkgconfig prettyunits progress purrr R6 RColorBrewer Rcpp readr rlang S7 scales stringi stringr tibble tidyr tidyselect timechange tzdb utf8 vctrs viridisLite vroom withr

MRMhub

Rendered frommrmhub.rmdusingknitr::rmarkdown

Last update: 2026-10-04
Started: 2026-06-23

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Access slots of a 'MRMhubExperiment' object via $ syntax	$,MRMhubExperiment-method
Add metadata to an 'MRMhubExperiment' object	add_metadata
Launch the MRMhub Workflow Builder	build_workflow
Calculate average molecular weight from chemical formulas	calc_average_molweight
Calculate external calibration curve results	calc_calibration_results
Derive isotopic interference relationships	calc_isotopic_interferences
Calculate quality control (QC) metrics for features	calc_qc_metrics
Calibrate feature values using a reference sample	calibrate_by_reference
Check MRMhub setup	check_setup
Batch centering correction	correct_batch_centering
ComBat batch correction	correct_batch_combat
SERRF batch correction	correct_batch_serrf
Correct declared (custom) interferences	correct_custom_interferences
Drift correction by custom function	correct_drift
Drift correction by cubic spline smoothing	correct_drift_cubicspline
Drift correction by generalized additive model (GAM) smoothing	correct_drift_gam
Drift correction by Gaussian kernel smoothing	correct_drift_gaussiankernel
Drift correction by LOESS smoothing	correct_drift_loess
Manual isotopic interference correction	correct_interference_manual
Correct automatically derived isotopic interferences	correct_isotopic_interferences
Percent coefficient of variation (%CV)	cv
Percent coefficient of variation (%CV) based on log-transformation	cv_log
Load an example 'MRMhubExperiment' dataset	data_load_example
Sum up feature intensities per analyte	data_sum_features
Get list of analyses classified as technical outliers	detect_outlier_pca
Exclude analyses from the dataset	exclude_analyses
Exclude features from the dataset	exclude_features
Feature filtering based on QC criteria	filter_features_qc
Cubic spline smoothing helper function	fun_cspline
Generalized additive model (GAM) smoothing helper function	fun_gam_smooth
Gaussian kernel smoothing helper function	fun_gauss.kernel.smooth
Loess smoothing helper function	fun_loess
Generate a runnable Quarto (.qmd) mrmhub workflow	generate_workflow_qmd
Get the end time of the analysis sequence	get_analyis_end
Get the start time of the analysis sequence	get_analyis_start
Get the number of analysis breaks in the analysis	get_analysis_breaks
Get the number of analyses in the dataset	get_analysis_count
Get the total duration of the analysis	get_analysis_duration
Get the annotated or the originally imported analytical data	get_analyticaldata
Get the start and end analysis numbers of specified batches	get_batch_boundaries
Get calibration metrics	get_calibration_metrics
Get the number of features in the dataset	get_feature_count
Get feature IDs	get_featurelist
Get Tukey's IQR fences	get_iqr_tails
Get MAD-based tails	get_mad_tails
Get outlier bounds via different methods	get_outlier_bounds
Retrieve QC bias and variability metrics	get_qc_bias_variability
Linear regression statistics of response curves	get_response_curve_stats
Get the median run time	get_runtime_median
Import analysis results from long-format CSV files	import_data_csv_long
Import analysis results from plain wide-format CSV files	import_data_csv_wide
Import Agilent MassHunter Quantitative Analysis CSV files	import_data_masshunter
Import MRMhub peak integration results	import_data_mrmhub
Import data from an mzTab-M file	import_data_mztab
Import Skyline peak integration results	import_data_skyline
Import analysis metadata	import_metadata_analyses
Import feature metadata	import_metadata_features
Retrieve metadata from imported analysis data	import_metadata_from_data
Import internal standards (ISTD) metadata	import_metadata_istds
Import metadata from a MRMhub Metadata Organizer file	import_metadata_msorganiser
Import calibration curves metadata	import_metadata_qcconcentrations
Import response curves metadata	import_metadata_responsecurves
Valid MRM-pattern labels	licar_pattern_choices
Plasma lipidomics dataset with metadata	lipidomics_dataset
Enable coloured mrmhub console output in notebooks	mrmhub_enable_cli_color
Report the global MRMhub plot defaults	mrmhub_get_plot_defaults
Clear the global MRMhub plot defaults	mrmhub_reset_plot_defaults
Set global default appearance for MRMhub plots	mrmhub_set_plot_defaults
Detailed processing and metadata report for a 'MRMhubExperiment'	mrmhub_status
Constructor for the 'MRMhubExperiment' object	MRMhubExperiment
S4 class representing the MRMhub dataset	MRMhubExperiment-class
Normalize feature intensities using internal standards	normalize_by_istd
Get lipid class, species and transition names	parse_lipid_feature_names
Reads and parses one Agilent MassHunter Quant CSV result file	parse_masshunter_csv
Parses MRMhub peak integration results into a tibble	parse_mrmhub_result
Parses a plain long CSV file	parse_plain_long_csv
Parses a plain wide CSV file	parse_plain_wide_csv
Parses skyline peak integration results into a tibble	parse_skyline_result
Plot abundance profile	plot_abundanceprofile
Plot calibration curves	plot_calibrationcurves
Plot highly correlated feature pairs	plot_feature_correlations
Plot the results of interference correction	plot_interference_correction
Plot standardized feature intensities grouped by QC type	plot_matrixeffects
Compare feature variability before and after normalization	plot_normalization_qc
PCA plot for quality control	plot_pca
Plot PCA loadings	plot_pca_loading
Plot the magnitude of interference correction as a histogram	plot_qc_interference_impact
Plot QC filtering summary by feature class	plot_qc_summary_byclass
Plot overall QC filtering summary	plot_qc_summary_overall
Comparison of two feature QC metrics variables	plot_qcmetrics_comparison
Plot response curves	plot_responsecurves
Relative log abundance (RLA) plot	plot_rla_boxplot
Plot retention time versus chain length and saturation	plot_rt_vs_chain
RunScatter plot	plot_runscatter
RunSequence plot	plot_runsequence
Pooled percent relative standard deviation (%RSD) across groups	pooled_rsd
Pooled standard deviation across groups	pooled_sd
LC-MS dataset with external calibration curve and metadata	quant_lcms_dataset
Calculate concentrations based on external calibration	quantify_by_calibration
Calculate analyte concentrations using internal standards	quantify_by_istd
Read a complete 'MRMhubExperiment' from an RDS file	read_dataset_rds
Export data to a CSV file	save_dataset_csv
Export an experiment to mzTab-M (HUPO-PSI)	save_dataset_mztab
Save a complete 'MRMhubExperiment' as an RDS file	save_dataset_rds
Export an experiment to a Bioconductor SummarizedExperiment	save_dataset_summarizedexperiment
Save feature QC metrics to CSV	save_feature_qc_metrics
Saves a MRMhub Metadata Organizer template	save_metadata_msorganiser_template
Saves an Excel (xlsx) file with metadata templates	save_metadata_templates
Save a plot to a file	save_plot
Write a data-processing report (Excel)	save_report_xlsx
Set analysis order	set_analysis_order
Set default variable to be used as feature raw signal value	set_intensity_var
Set feature classes from lipid names	set_lipid_class
Summarize interference relationships	summarize_interferences