# R interface to EBI MGnify metagenomics resource

## Documentation for package ‘MGnifyR’ version 1.0.0

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

## Help Pages

MGnifyR-package | 'MGnifyR' Package.
authTok | MgnifyClient accessors and mutators
authTok-method | MgnifyClient accessors and mutators
authTok<- | MgnifyClient accessors and mutators
authTok<--method | MgnifyClient accessors and mutators
cacheDir | MgnifyClient accessors and mutators
cacheDir-method | MgnifyClient accessors and mutators
cacheDir<- | MgnifyClient accessors and mutators
cacheDir<--method | MgnifyClient accessors and mutators
clearCache | MgnifyClient accessors and mutators
clearCache-method | MgnifyClient accessors and mutators
clearCache<- | MgnifyClient accessors and mutators
clearCache<--method | MgnifyClient accessors and mutators
databaseUrl | MgnifyClient accessors and mutators
databaseUrl-method | MgnifyClient accessors and mutators
databaseUrl<- | MgnifyClient accessors and mutators
databaseUrl<--method | MgnifyClient accessors and mutators
deprecate | These functions will be deprecated. Please use other functions instead.
doQuery | Search MGnify database for studies, samples, runs, analyses, biomes, assemblies, and genomes.
doQuery-method | Search MGnify database for studies, samples, runs, analyses, biomes, assemblies, and genomes.
getData | Versatile function to retrieve raw results
getData-method | Versatile function to retrieve raw results
getFile | Download any MGnify files, also including processed reads and identified protein sequences
getFile-method | Download any MGnify files, also including processed reads and identified protein sequences
getMetadata | Get all Study, Sample and Analysis metadata for the supplied analyses accessions
getMetadata-method | Get all Study, Sample and Analysis metadata for the supplied analyses accessions
getResult | Get microbial and/or functional profiling data for a list of accessions
getResult-method | Get microbial and/or functional profiling data for a list of accessions
MgnifyClient | Constructor for creating a MgnifyClient object to allow the access to MGnify database.
MgnifyClient-accessors | MgnifyClient accessors and mutators
MgnifyClient-class | Constructor for creating a MgnifyClient object to allow the access to MGnify database.
MGnifyR | 'MGnifyR' Package.
mgnify_analyses_from_samples | These functions will be deprecated. Please use other functions instead.
mgnify_analyses_from_studies | These functions will be deprecated. Please use other functions instead.
mgnify_client | These functions will be deprecated. Please use other functions instead.
mgnify_download | These functions will be deprecated. Please use other functions instead.
mgnify_get_analyses_metadata | These functions will be deprecated. Please use other functions instead.
mgnify_get_analyses_phyloseq | These functions will be deprecated. Please use other functions instead.
mgnify_get_analyses_results | These functions will be deprecated. Please use other functions instead.
mgnify_get_download_urls | These functions will be deprecated. Please use other functions instead.
mgnify_query | These functions will be deprecated. Please use other functions instead.
mgnify_retrieve_json | These functions will be deprecated. Please use other functions instead.
searchAnalysis | Look up analysis accession IDs for one or more study or sample accessions
searchAnalysis-method | Look up analysis accession IDs for one or more study or sample accessions
searchFile | Download any MGnify files, also including processed reads and identified protein sequences
searchFile-method | Download any MGnify files, also including processed reads and identified protein sequences
showWarnings | MgnifyClient accessors and mutators
showWarnings-method | MgnifyClient accessors and mutators
showWarnings<- | MgnifyClient accessors and mutators
showWarnings<--method | MgnifyClient accessors and mutators
useCache | MgnifyClient accessors and mutators
useCache-method | MgnifyClient accessors and mutators
useCache<- | MgnifyClient accessors and mutators
useCache<--method | MgnifyClient accessors and mutators
verbose | MgnifyClient accessors and mutators
verbose-method | MgnifyClient accessors and mutators
verbose<- | MgnifyClient accessors and mutators
verbose<--method | MgnifyClient accessors and mutators