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All functions

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