# Metabolite Mashing with R

## Documentation for package ‘MetMashR’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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 --

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
upset_filters | UpSet chart filter helper functions
upset_intersections | UpSet chart filter helper functions
upset_max_groups | UpSet chart filter helper functions
upset_min_groups | UpSet chart filter helper functions
upset_min_size | UpSet chart filter helper functions

## -- 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