View source: R/curatedMetagenomicData.R
curatedMetagenomicData | R Documentation |
To access curated metagenomic data users will use curatedMetagenomicData()
after "shopping" the sampleMetadata data.frame
for resources they are
interested in. The dryrun
argument allows users to perfect a query prior to
returning resources. When dryrun = TRUE
, matched resources will be printed
before they are returned invisibly as a character vector. When
dryrun = FALSE
, a list
of resources containing
SummarizedExperiment
and/or
TreeSummarizedExperiment
objects, each with corresponding sample metadata, is returned. Multiple
resources can be returned simultaneously and if there is more than one date
corresponding to a resource, the most recent one is selected automatically.
Finally, if a relative_abundance
resource is requested and counts = TRUE
,
relative abundance proportions will be multiplied by read depth and rounded
to the nearest integer.
curatedMetagenomicData(
pattern,
dryrun = TRUE,
counts = FALSE,
rownames = "long"
)
pattern |
regular expression pattern to look for in the titles of
resources available in curatedMetagenomicData; |
dryrun |
if |
counts |
if |
rownames |
the type of |
Above "resources" refers to resources that exists in Bioconductor's
ExperimentHub service. In the context of curatedMetagenomicData, these are
study-level (sparse) matrix objects used to create
SummarizedExperiment
and/or
TreeSummarizedExperiment
objects that are ultimately returned as the list
of resources. Only the
gene_families
dataType
(see returnSamples) is stored as a sparse matrix
in ExperimentHub – this has no practical consequences for users and is done
to optimize storage. When searching for "resources", users will use the
study_name
value from the sampleMetadata data.frame
.
if dryrun = TRUE
, a character vector of resource names is returned
invisibly; if dryrun = FALSE
, a list
of resources is returned
mergeData, returnSamples, sampleMetadata
curatedMetagenomicData("AsnicarF_20.+")
curatedMetagenomicData("AsnicarF_2017.relative_abundance", dryrun = FALSE)
curatedMetagenomicData("AsnicarF_20.+.relative_abundance", dryrun = FALSE, counts = TRUE)
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