Run EnrichR on SCE object
runEnrichR(
inSCE,
features,
analysisName,
db = NULL,
by = "rownames",
featureName = NULL
)
A SingleCellExperiment object.
Character vector, selected genes for enrichment analysis.
A string that identifies each specific analysis.
Character vector. Selected database name(s) from the enrichR
database list. If NULL
then EnrichR will be run on all the available
databases on the enrichR database. See details. Default NULL
Character. From where should we find the features
?
"rownames"
for from rownames(inSCE)
, otherwise, from a column
of feature metadata (rowData(inSCE)[[by]]
). See details. Default
"rownames"
.
Character. Indicates the actual feature identifiers to be
passed to EnrichR. Can be "rownames"
, a column in feature metadata
(rowData(inSCE)[[featureName]]
), or a character vector with its length
equals to nrow(inSCE)
. See details. Default "rownames"
.
Updates inSCE
metadata with a data.frame of enrichment terms
overlapping in the respective databases along with p-values, z-scores etc.
EnrichR works by querying the specified features
to its online
databases, thus it requires the Internet connection.
Available db
options could be shown by running
enrichR::listEnrichrDbs()$libraryName
This function checks for the existence of features in the SCE object. When
features
do not have a match in rownames(inSCE)
, users may
try to specify by
to pass the check.
EnrichR expects gene symbols/names as the input (i.e. Ensembl ID might not
work). When specified features
are not qualified for this, users may
try to specify featureName
to change the identifier type to pass to
EnrichR.
data("mouseBrainSubsetSCE")
if (Biobase::testBioCConnection()) {
mouseBrainSubsetSCE <- runEnrichR(mouseBrainSubsetSCE, features = "Cmtm5",
db = "GO_Cellular_Component_2017",
analysisName = "analysis1")
}
#> Uploading data to Enrichr... Done.
#> Querying GO_Cellular_Component_2017... Done.
#> Parsing results... Done.