To return samples across studies, users will use
returnSamples() along with
data.frame subset to include only desired samples and
metadata. The subset sampleMetadata
data.frame will be used to get the
desired resources, mergeData will be used to merge them, and the subset
data.frame will be used again to subset the
object to include only desired samples and metadata.
returnSamples(sampleMetadata, dataType, counts = FALSE, rownames = "long")
the data type to be returned; one of the following:
the type of
At present, curatedMetagenomicData resources exists only as entire studies which requires potentially getting many resources for a limited number of samples. Furthermore, because it is necessary to use mergeData internally, the same caveats detailed under Details in mergeData apply here.
dataType = "relative_abundance", a
object is returned; otherwise, a
object is returned
sampleMetadata |> dplyr::filter(age >= 18) |> dplyr::filter(!base::is.na(alcohol)) |> dplyr::filter(body_site == "stool") |> dplyr::select(where(~ !base::all(base::is.na(.x)))) |> returnSamples("relative_abundance")
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.