Package: MetMashR 1.7.2

Gavin Rhys Lloyd

MetMashR: Metabolite Mashing with R

A package to merge, filter sort, organise and otherwise mash together metabolite annotation tables. Metabolite annotations can be imported from multiple sources (software) and combined using workflow steps based on S4 class templates derived from the `struct` package. Other modular workflow steps such as filtering, merging, splitting, normalisation and rest-api queries are included.

Authors:Gavin Rhys Lloyd [aut, cre], Ralf Johannes Maria Weber [aut]

MetMashR_1.7.2.tar.gz
MetMashR_1.7.2.zip(r-4.7-any)MetMashR_1.7.2.zip(r-4.6-any)MetMashR_1.7.2.zip(r-4.5-any)
MetMashR_1.7.2.tgz(r-4.6-any)MetMashR_1.7.2.tgz(r-4.5-any)
MetMashR_1.7.2.tar.gz(r-4.7-any)MetMashR_1.7.2.tar.gz(r-4.6-any)
MetMashR_1.7.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MetMashR/json (API)

# Install 'MetMashR' in R:
install.packages('MetMashR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/computational-metabolomics/metmashr/issues

Pkgdown/docs site:https://computational-metabolomics.github.io

On BioConductor:MetMashR-1.7.1(bioc 3.24)MetMashR-1.6.0(bioc 3.23)

workflowstepmetabolomicskegg

5.78 score 3 stars 10 scripts 304 downloads 112 exports 62 dependencies

Last updated from:5deeed2ee4. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE257
linux-develOK456
source / vignettesOK546
linux-releaseOK446
macos-releaseOK270
macos-oldrelOK291
windows-develOK339
windows-releaseOK331
windows-oldrelOK314
wasm-releaseOK217

Exports:add_columnsadd_labelsannotation_bar_chartannotation_databaseannotation_histogramannotation_histogram2dannotation_pie_chartannotation_sourceannotation_tableannotation_upset_chartannotation_venn_chartAnnotationDb_databaseAnnotationDb_selectBiocFileCache_databasecache_as_iscalc_ppm_diffcalc_rt_diffcd_sourcechart_plotchebi_lookupcheck_for_columnsclassyfire_batch_lookupclassyfire_lookupcombine_columnscombine_recordscombine_sourcesCompoundDb_sourcecompute_columncompute_meancompute_mediancompute_modecompute_recordcount_recordscts_lite_lookupdatabase_lookupeutils_lookupexcel_databasefilter_labelsfilter_nafilter_rangefilter_recordsfilter_vennfusefuse_uniquegithub_fileGO_databasegreek_dictionaryhmdb_lookupid_countsimport_sourceis_writablekegg_lookuplcms_tablelipidmaps_databaselipidmaps_lookupls_sourcemodel_applymodel_predictmodel_trainmspurity_sourceMTox700plus_databasemwb_compound_lookupmwb_refmet_databasemwb_refmet_lookupmwb_structuremwb_study_sourcemz_matchmzrt_matchnormalise_lipidsnormalise_stringsnothingopsin_lookupPathBank_metabolite_databasepivot_columnsprioritiseprioritise_columnspubchem_compound_lookuppubchem_id_exchangepubchem_property_lookuppubchem_structurepubchem_widgetracemic_dictionaryrdata_databaserds_cacherds_databaseread_databaseread_sourceremove_columnsrename_columnsrequired_colsrest_apirt_matchselect_columnsselect_exactselect_gradeselect_matchselect_maxselect_minsplit_columnsplit_recordssqlite_databasetrim_whitespacetripeptide_dictionaryunique_recordsunzip_before_cacheupset_intersectionsupset_max_groupsupset_min_groupsupset_min_sizevertical_joinwhereverwrite_database

Dependencies:abindaskpassBiobaseBiocGenericsclicpp11curlDelayedArraydplyrevaluatefarvergenericsGenomicRangesggplot2ggthemesgluegtablehighrhttrhttr2IRangesisobandjsonliteknitrlabelinglatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigplyrpurrrR6RColorBrewerRcpprlangS4ArraysS4VectorsS7scalesSeqinfoSparseArraystringistringrstructSummarizedExperimentsystibbletidyselectutf8vctrsviridisLitewithrxfunxml2XVectoryaml

Case study: reimplementing the Metabolites Merging Strategy with MetMashR
Introduction | Importing the source data | Building the model sequence | Normalising synonyms | Translation and merging (MMS Step 1) | Attribute retrieval (MMS Step 2) | Manual curation (MMS Step 3) | The complete sequence | What the harmonised tables look like | Comparison against the published result | Characterising the mismatch | Learnings and Benefits of MetMashR | References | Session Info
Rendered frommms_case_study.Rmdusingknitr::rmarkdown

Last update: 2026-10-01
Started: 2026-10-01

Annotation of mixtures of standards
Getting Started | Introduction | Input data | Importing the annotations | Importing Compound Discoverer annotations | Importing LipidSearch annotations | Exploratory analysis of annotation sources | Combining Annotation Sources | Adding identifiers | Improving ID coverage | Comparison with the true mixtures | Importing the standard mixture tables | Identifiers for the standards | Comparison of standards and annotations | Session Info
Rendered fromannotate_mixtures.Rmdusingknitr::rmarkdown

Last update: 2026-10-01
Started: 2024-01-19

Exploring the MTox700+ library
Getting Started | Introduction | Importing the MTox700+ database | Exploring the chemical space | Exploring the biological space | Importing PathBank | Comparing PathBank and MTox700+ | Combining MTox700+ with PathBank | Combining records | Session Info
Rendered fromexploring_mtox.Rmdusingknitr::rmarkdown

Last update: 2026-10-01
Started: 2024-01-19

Extending MetMashR
Introduction | Getting Started | Example study | Annotation Sources | Adding new annotation sources | The class definition | The calling function | The import method | Using the new source | Adding annotation workflow steps | Empty column removal | Suffix removal | Metabolite mashing | Summary | Session Info
Rendered fromExtending_MetMashR.Rmdusingknitr::rmarkdown

Last update: 2026-10-01
Started: 2024-01-19

Using MetMashR
Introduction | Statistics in R using Class Templates (struct) | Getting Started | Annotation Sources | Annotation Tables | Annotation Databases | Cached databases | Annotation Mashing | Importing sources | Filtering / Cleaning | LCMS peak matching | REST APIs | Dictionaries | Combining Records | Session Info
Rendered fromusing_MetMashR.Rmdusingknitr::rmarkdown

Last update: 2026-10-01
Started: 2024-01-19

Readme and manuals

Help Manual

Help pageTopics
Add columnsadd_columns
Add column of labelsadd_labels
Annotation bar chartannotation_bar_chart
An annotation databaseannotation_database
Annotation histogramannotation_histogram
Annotation 2D histogramannotation_histogram2d
Annotation pie chartannotation_pie_chart
An annotation sourceannotation_source
An annotation tableannotation_table
Annotation UpSet chartannotation_upset_chart
Annotation venn chartannotation_venn_chart
AnnotationDb databaseAnnotationDb_database
Select columns from AnnotationDb databaseAnnotationDb_select
Cached databaseBiocFileCache_database
Cache file with no changes using BiocFileCachecache_as_is
Calculate ppm differencecalc_ppm_diff
Calculate RT differencecalc_rt_diff
LCMS tablecd_source
chart_plot methodchart_plot chart_plot,annotation_bar_chart,annotation_source-method chart_plot,annotation_histogram,annotation_source-method chart_plot,annotation_histogram2d,annotation_source-method chart_plot,annotation_pie_chart,annotation_source-method chart_plot,annotation_upset_chart,annotation_source-method chart_plot,annotation_upset_chart,list-method chart_plot,annotation_venn_chart,annotation_source-method chart_plot,annotation_venn_chart,list-method chart_plot,mwb_structure,annotation_source-method chart_plot,pubchem_structure,annotation_source-method chart_plot,pubchem_widget,annotation_source-method
ID/synonym lookup via ChEBIchebi_lookup
Check for columns in an 'annotation_source'check_for_columns check_for_columns,annotation_source-method
ClassyFire batch lookupclassyfire_batch_lookup
Query ClassyFire databaseclassyfire_lookup
Combine columnscombine_columns
Combine annotation records (rows)combine_records
Combine records helper functionscombine_records_helper_functions compute_mean compute_median compute_mode count_records fuse fuse_unique nothing prioritise select_exact select_grade select_match select_max select_min
Combine annotation sources (tables)combine_sources
Import CompDB sourceCompoundDb_source
Compute a columncompute_column
Compute a value for a recordcompute_record
Batch lookup via CTS-Litects_lite_lookup
ID lookup by databasedatabase_lookup
NCBI E-utils queryeutils_lookup
Excel databaseexcel_database
Filter by factor labelsfilter_labels
Filter by missing valuesfilter_na
Filter by rangefilter_range
Filter rowsfilter_records
Filter by factor levelsfilter_venn
GitHub filegithub_file
GO.dbGO_database
Greek dictionarygreek_dictionary
Compound ID lookup via pubchemhmdb_lookup
id countsid_counts
Import_sourceimport_source
Is database writableis_writable is_writable,annotation_database-method is_writable,rdata_database-method
Convert to or from kegg identifierskegg_lookup
LCMS tablelcms_table
LIPID MAPS databaselipidmaps_database
LipidMaps api lookuplipidmaps_lookup
LCMS tablels_source
Apply methodmodel_apply model_apply,add_columns,annotation_source-method model_apply,add_labels,annotation_source-method model_apply,AnnotationDb_select,annotation_source-method model_apply,calc_ppm_diff,annotation_table-method model_apply,calc_rt_diff,annotation_table-method model_apply,chebi_lookup,annotation_source-method model_apply,classyfire_batch_lookup,annotation_source-method model_apply,combine_columns,annotation_source-method model_apply,combine_records,annotation_source-method model_apply,combine_sources,annotation_source-method model_apply,combine_sources,list-method model_apply,CompoundDb_source,annotation_source-method model_apply,compute_column,annotation_source-method model_apply,compute_record,annotation_source-method model_apply,cts_lite_lookup,annotation_source-method model_apply,database_lookup,annotation_source-method model_apply,filter_labels,annotation_source-method model_apply,filter_na,annotation_source-method model_apply,filter_range,annotation_source-method model_apply,filter_records,annotation_source-method model_apply,filter_venn,annotation_source-method model_apply,id_counts,annotation_source-method model_apply,import_source,annotation_source-method model_apply,kegg_lookup,annotation_source-method model_apply,model,annotation_source-method model_apply,model,list-method model_apply,model_seq,annotation_source-method model_apply,model_seq,list-method model_apply,mzrt_match,lcms_table-method model_apply,mz_match,annotation_source-method model_apply,normalise_lipids,annotation_source-method model_apply,normalise_strings,annotation_source-method model_apply,pivot_columns,annotation_source-method model_apply,prioritise_columns,annotation_source-method model_apply,pubchem_id_exchange,annotation_source-method model_apply,remove_columns,annotation_source-method model_apply,rename_columns,annotation_source-method model_apply,rest_api,annotation_source-method model_apply,rt_match,annotation_table-method model_apply,select_columns,annotation_source-method model_apply,split_column,annotation_source-method model_apply,split_records,annotation_source-method model_apply,trim_whitespace,annotation_source-method model_apply,unique_records,annotation_source-method model_predict model_predict,classyfire_batch_lookup,annotation_source-method model_predict,pubchem_id_exchange,annotation_source-method model_train model_train,classyfire_batch_lookup,annotation_source-method model_train,pubchem_id_exchange,annotation_source-method
msPurity sourcemspurity_source
MTox700plus_databaseMTox700plus_database
Convert to/from kegg identifiersmwb_compound_lookup
mwb_refmet_databasemwb_refmet_database
Metabolomics Workbench RefMet lookupmwb_refmet_lookup
MWB molecular structuremwb_structure
Metabolomics Workbench study sourcemwb_study_source
mz matchingmz_match
mz matchingmzrt_match
Normalise Lipids nomenclaturenormalise_lipids
Normalise stringnormalise_strings
Compound ID lookup via OPSINopsin_lookup
PathBank_metabolite_databasePathBank_metabolite_database
Pivot longerpivot_columns
Combine several columns into a single column.prioritise_columns
Compound ID lookup via PubChempubchem_compound_lookup
PubChem ID Exchange via PUGpubchem_id_exchange
Compound property lookup via pubchempubchem_property_lookup
PubChem molecular structurepubchem_structure
PubChem widgetpubchem_widget
Racemic dictionaryracemic_dictionary
rdata databaserdata_database
rds cacherds_cache
rds databaserds_database
Read a databaseread_database read_database,AnnotationDb_database-method read_database,annotation_database-method read_database,BiocFileCache_database-method read_database,excel_database-method read_database,github_file-method read_database,MTox700plus_database-method read_database,mwb_refmet_database-method read_database,PathBank_metabolite_database-method read_database,rdata_database-method read_database,rds_database-method read_database,sqlite_database-method
Import annotation sourceread_source read_source,annotation_database-method read_source,annotation_source-method read_source,cd_source-method read_source,ls_source-method read_source,mspurity_source-method read_source,mwb_study_source-method
Select columnsremove_columns
Select columnsrename_columns
Required columns in an annotation sourcerequired_cols required_cols,annotation_source-method
rest_apirest_api
rt matchingrt_match
Select columnsselect_columns
Split a columnsplit_column
Expand recordssplit_records
SQLite databasesqlite_database
Trim whitespacetrim_whitespace
Tripeptide dictionarytripeptide_dictionary
Keep unique_recordsunique_records
Unzip file before caching with BiocFileCache_databaseunzip_before_cache
UpSet chart filter helper functionsupset_filters upset_intersections upset_max_groups upset_min_groups upset_min_size
Join sources verticallyvertical_join vertical_join,annotation_source,annotation_source-method vertical_join,list,missing-method
Filter helper function to select recordswherever
Write to a databasewrite_database write_database,annotation_database-method write_database,rds_database-method write_database,sqlite_database-method