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