Function reference • MGnifyR

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 analyses 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