Get a collection from the Microbiome Dataset. The collection will be returned as an AbundanceData, phyloseq, or Collection object.
Usage
getCollection(
object,
collectionName,
format = c("AbundanceData", "phyloseq", "Collection"),
continuousMetadataOnly = c(FALSE, TRUE)
)
# S4 method for MbioDataset
getCollection(
object,
collectionName = character(0),
format = c("AbundanceData", "phyloseq", "Collection"),
continuousMetadataOnly = c(FALSE, TRUE)
)Arguments
- object
A Microbiome Dataset
- collectionName
The name of the collection to return
- format
The format of the collection to return. Currently supported options are "AbundanceData", "phyloseq" and "Collection".
- continuousMetadataOnly
If TRUE, only continuous metadata will be returned. If FALSE, all metadata will be returned.
Value
An AbundanceData, phyloseq, or Collection object representing the collection and any associated study metadata
Examples
genus <- getCollection(
microbiomeData::DiabImmune,
"16S (V4) Genus (Relative taxonomic abundance analysis)"
)
genus_phyloseq <- getCollection(
microbiomeData::DiabImmune,
"16S (V4) Genus (Relative taxonomic abundance analysis)",
format = "phyloseq"
)
## to pass to correlation method, we want only continuous metadata
genus_continuous <- getCollection(
microbiomeData::DiabImmune,
"16S (V4) Genus (Relative taxonomic abundance analysis)",
continuousMetadataOnly = TRUE
)
## with no metadata
genus_collection <- getCollection(
microbiomeData::DiabImmune,
"16S (V4) Genus (Relative taxonomic abundance analysis)",
format = "Collection"
)