R interface to EBI MGnify metagenomics resource

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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