Metabolite Mashing with R
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Documentation for package ‘MetMashR’ version 1.1.0
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A B C D E F G H I K L M N O P R S T U V W
-- A --
| add_columns | Add columns |
| add_labels | Add column of labels |
| AnnotationDb_database | AnnotationDb database |
| AnnotationDb_select | Select columns from AnnotationDb database |
| annotation_bar_chart | Annotation bar chart |
| annotation_database | An annotation database |
| annotation_histogram | Annotation histogram |
| annotation_histogram2d | Annotation 2D histogram |
| annotation_pie_chart | Annotation pie chart |
| annotation_source | An annotation source |
| annotation_table | An annotation table |
| annotation_upset_chart | Annotation UpSet chart |
| annotation_venn_chart | Annotation venn chart |
-- B --
| BiocFileCache_database | Cached database |
-- C --
| cache_as_is | Cache file with no changes using BiocFileCache |
| calc_ppm_diff | Calculate ppm difference |
| calc_rt_diff | Calculate RT difference |
| cd_source | LCMS table |
| chart_plot | chart_plot method |
| chart_plot-method | chart_plot method |
| check_for_columns | Check for columns in an 'annotation_source' |
| check_for_columns-method | Check for columns in an 'annotation_source' |
| classyfire_lookup | Query ClassyFire database |
| combine_columns | Combine columns |
| combine_records | Combine annotation records (rows) |
| combine_records_helper_functions | Combine records helper functions |
| combine_sources | Combine annotation sources (tables) |
| CompoundDb_source | Import CompDB source |
| compute_column | Compute a column |
| compute_mean | Combine records helper functions |
| compute_median | Combine records helper functions |
| compute_mode | Combine records helper functions |
| compute_record | Compute a value for a record |
| count_records | Combine records helper functions |
-- D --
| database_lookup | ID lookup by database |
-- E --
| eutils_lookup | NCBI E-utils query |
| excel_database | Excel database |
-- F --
| filter_labels | Filter by factor labels |
| filter_na | Filter by missing values |
| filter_range | Filter by range |
| filter_records | Filter rows |
| filter_venn | Filter by factor levels |
| fuse | Combine records helper functions |
| fuse_unique | Combine records helper functions |
-- G --
| github_file | GitHub file |
| GO_database | GO.db |
| greek_dictionary | Greek dictionary |
-- H --
| hmdb_lookup | Compound ID lookup via pubchem |
-- I --
| id_counts | id counts |
| import_source | Import_source |
| is_writable | Is database writable |
| is_writable-method | Is database writable |
-- K --
| kegg_lookup | Convert to or from kegg identifiers |
-- L --
| lcms_table | LCMS table |
| lipidmaps_lookup | LipidMaps api lookup |
| ls_source | LCMS table |
-- M --
| model_apply | Apply method |
| model_apply-method | Apply method |
| mspurity_source | msPurity source |
| MTox700plus_database | MTox700plus_database |
| mwb_compound_lookup | Convert to/from kegg identifiers |
| mwb_refmet_database | mwb_refmet_database |
| mwb_structure | MWB molecular structure |
| mzrt_match | mz matching |
| mz_match | mz matching |
-- N --
| normalise_lipids | Normalise Lipids nomenclature |
| normalise_strings | Normalise string |
| nothing | Combine records helper functions |
-- O --
| openbabel_structure | OpenBabel molecular structure |
| opsin_lookup | Compound ID lookup via OPSIN |
-- P --
| PathBank_metabolite_database | PathBank_metabolite_database |
| pivot_columns | Pivot longer |
| prioritise | Combine records helper functions |
| prioritise_columns | Combine several columns into a single column. |
| pubchem_compound_lookup | Compound ID lookup via PubChem |
| pubchem_property_lookup | Compound property lookup via pubchem |
| pubchem_structure | PubChem molecular structure |
| pubchem_widget | PubChem widget |
-- R --
| racemic_dictionary | Racemic dictionary |
| rdata_database | rdata database |
| rds_cache | rds cache |
| rds_database | rds database |
| read_database | Read a database |
| read_database-method | Read a database |
| read_source | Import annotation source |
| read_source-method | Import annotation source |
| remove_columns | Select columns |
| rename_columns | Select columns |
| required_cols | Required columns in an annotation source |
| required_cols-method | Required columns in an annotation source |
| rest_api | rest_api |
| rt_match | rt matching |
-- S --
| select_columns | Select columns |
| select_exact | Combine records helper functions |
| select_grade | Combine records helper functions |
| select_match | Combine records helper functions |
| select_max | Combine records helper functions |
| select_min | Combine records helper functions |
| split_column | Split a column |
| split_records | Expand records |
| sqlite_database | SQLite database |
-- T --
| trim_whitespace | Trim whitespace |
| tripeptide_dictionary | Tripeptide dictionary |
-- U --
| unique_records | Keep unique_records |
| unzip_before_cache | Unzip file before caching with BiocFileCache_database |
-- V --
| vertical_join | Join sources vertically |
| vertical_join-method | Join sources vertically |
-- W --
| wherever | Filter helper function to select records |
| write_database | Write to a database |
| write_database-method | Write to a database |