Package index • MetMashR

Annotation sources

An annotation source is the dataset object used by all MetMashR objects. Different types of source have been defined, depending on the intended use of the data.

CompoundDb_source(): Import CompDB source

annotation_source(): An annotation source

cd_source(): LCMS table

import_source(): Import_source

ls_source(): LCMS table

mspurity_source(): msPurity source

read_source(): Import annotation source

Annotation tables

Annotation tables represent the data imported from a source that includes experimentally measured data. Annotation tables are extended to support the specifics of an analytical platform used to collect the data.

annotation_table(): An annotation table

lcms_table(): LCMS table

Annotation databases

Annotation databases are (often remote) sources of annotation related meta data, such as molecular identifiers, pathways etc.

AnnotationDb_database(): AnnotationDb database

BiocFileCache_database(): Cached database

GO_database(): GO.db

MTox700plus_database(): MTox700plus_database

PathBank_metabolite_database(): PathBank_metabolite_database

annotation_database(): An annotation database

excel_database(): Excel database

mwb_refmet_database(): mwb_refmet_database

rdata_database(): rdata database

rds_database(): rds database

read_database(): Read a database

sqlite_database(): SQLite database

write_database(): Write to a database

rds_cache(): rds cache

github_file(): GitHub file

is_writable(): Is database writable

REST API interfaces

MetMashR includes a REST API object that has been extended to accomodate various services.

rest_api(): rest_api

classyfire_lookup(): Query ClassyFire database

database_lookup(): ID lookup by database

eutils_lookup(): NCBI E-utils query

hmdb_lookup(): Compound ID lookup via pubchem

kegg_lookup(): Convert to or from kegg identifiers

lipidmaps_lookup(): LipidMaps api lookup

mwb_compound_lookup(): Convert to/from kegg identifiers

opsin_lookup(): Compound ID lookup via OPSIN

pubchem_compound_lookup(): Compound ID lookup via PubChem

pubchem_property_lookup(): Compound property lookup via pubchem

Annotation table mashing

These models provide steps for cleaning, filtering, prioritising and combining annotation tables from different sources.

add_columns(): Add columns

add_labels(): Add column of labels

calc_ppm_diff(): Calculate ppm difference

calc_rt_diff(): Calculate RT difference

prioritise_columns(): Combine several columns into a single column.

combine_sources(): Combine annotation sources (tables)

vertical_join(): Join sources vertically

combine_records(): Combine annotation records (rows)

filter_labels(): Filter by factor labels

filter_range(): Filter by range

filter_na(): Filter by missing values

filter_venn(): Filter by factor levels

filter_records(): Filter rows

id_counts(): id counts

mz_match(): mz matching

rt_match(): rt matching

mzrt_match(): mz matching

normalise_lipids(): Normalise Lipids nomenclature

normalise_strings(): Normalise string

trim_whitespace(): Trim whitespace

combine_columns(): Combine columns

select_columns(): Select columns

remove_columns(): Select columns

split_column(): Split a column

split_records(): Expand records

AnnotationDb_select(): Select columns from AnnotationDb database

compute_column(): Compute a column

compute_record(): Compute a value for a record

pivot_columns(): Pivot longer

rename_columns(): Select columns

unique_records(): Keep unique_records

Combining records

Combining records is an important step in the annotation mashing workflow. These functions can be used with the combine_records function to merge the information for multiple records in different ways.

compute_mode() compute_mean() compute_median() fuse() select_max() select_min() select_match() select_exact() fuse_unique() prioritise() nothing() count_records() select_grade(): Combine records helper functions

Charts

Chart objects are wrappers around ggplot objects plots useful for exploring and visualising the information present in a table of annotations.

mwb_structure(): MWB molecular structure

openbabel_structure(): OpenBabel molecular structure

pubchem_structure(): PubChem molecular structure

annotation_bar_chart(): Annotation bar chart

annotation_pie_chart(): Annotation pie chart

annotation_upset_chart(): Annotation UpSet chart

annotation_venn_chart(): Annotation venn chart

annotation_histogram(): Annotation histogram

annotation_histogram2d(): Annotation 2D histogram

pubchem_widget(): PubChem widget

BiocFileCache_database helper functions

These functions can be used with BiocFileCache_database objects to modify a dowloaded resource before caching, or to parse the downloaded resource when retrieved from the cache.

cache_as_is(): Cache file with no changes using BiocFileCache

unzip_before_cache(): Unzip file before caching with BiocFileCache_database

Dictionaries for normalising strings

These lists define patterns and replacements to match when using the normalise_strings object.

greek_dictionary: Greek dictionary

racemic_dictionary: Racemic dictionary

tripeptide_dictionary: Tripeptide dictionary

Additional functions

Supporting functions are used by MetMashR

check_for_columns(): Check for columns in an annotation_source

required_cols(): Required columns in an annotation source

wherever(): Filter helper function to select records

chart_plot(<annotation_bar_chart>,<annotation_source>) chart_plot(<annotation_histogram>,<annotation_source>) chart_plot(<annotation_histogram2d>,<annotation_source>) chart_plot(<annotation_pie_chart>,<annotation_source>) chart_plot(<annotation_upset_chart>,<annotation_source>) chart_plot(<annotation_upset_chart>,<list>) chart_plot(<annotation_venn_chart>,<annotation_source>) chart_plot(<annotation_venn_chart>,<list>) chart_plot(<mwb_structure>,<annotation_source>) chart_plot(<openbabel_structure>,<character>) chart_plot(<openbabel_structure>,<annotation_source>) chart_plot(<pubchem_structure>,<annotation_source>) chart_plot(<pubchem_widget>,<annotation_source>): chart_plot method

model_apply(<model>,<annotation_source>) model_apply(<model>,<list>) model_apply(<model_seq>,<list>) model_apply(<model_seq>,<annotation_source>) model_apply(<AnnotationDb_select>,<annotation_source>) model_apply(<CompoundDb_source>,<annotation_source>) model_apply(<add_columns>,<annotation_source>) model_apply(<add_labels>,<annotation_source>) model_apply(<calc_ppm_diff>,<annotation_table>) model_apply(<calc_rt_diff>,<annotation_table>) model_apply(<rest_api>,<annotation_source>) model_apply(<combine_columns>,<annotation_source>) model_apply(<combine_records>,<annotation_source>) model_apply(<combine_sources>,<annotation_source>) model_apply(<combine_sources>,<list>) model_apply(<compute_column>,<annotation_source>) model_apply(<compute_record>,<annotation_source>) model_apply(<database_lookup>,<annotation_source>) model_apply(<split_records>,<annotation_source>) model_apply(<filter_labels>,<annotation_source>) model_apply(<filter_na>,<annotation_source>) model_apply(<filter_range>,<annotation_source>) model_apply(<filter_records>,<annotation_source>) model_apply(<filter_venn>,<annotation_source>) model_apply(<id_counts>,<annotation_source>) model_apply(<import_source>,<annotation_source>) model_apply(<kegg_lookup>,<annotation_source>) model_apply(<mspurity_source>,<lcms_table>) model_apply(<mz_match>,<annotation_source>) model_apply(<mzrt_match>,<lcms_table>) model_apply(<normalise_lipids>,<annotation_source>) model_apply(<normalise_strings>,<annotation_source>) model_apply(<pivot_columns>,<annotation_source>) model_apply(<prioritise_columns>,<annotation_source>) model_apply(<remove_columns>,<annotation_source>) model_apply(<rename_columns>,<annotation_source>) model_apply(<rt_match>,<annotation_table>) model_apply(<select_columns>,<annotation_source>) model_apply(<split_column>,<annotation_source>) model_apply(<trim_whitespace>,<annotation_source>) model_apply(<unique_records>,<annotation_source>): Apply method