getBMFeatureAnnos {scater} | R Documentation |
Use the biomaRt package to add feature annotation information to an
SingleCellExperiment
.
getBMFeatureAnnos(object, filters = "ensembl_transcript_id", attributes = c("ensembl_transcript_id", "ensembl_gene_id", feature_symbol, "chromosome_name", "transcript_biotype", "transcript_start", "transcript_end", "transcript_count"), feature_symbol = "mgi_symbol", feature_id = "ensembl_gene_id", biomart = "ENSEMBL_MART_ENSEMBL", dataset = "mmusculus_gene_ensembl", host = "www.ensembl.org")
object |
an |
filters |
character vector defining the "filters" terms to pass to the biomaRt::getBM function. |
attributes |
character vector defining the biomaRt attributes to pass to
the |
feature_symbol |
character string defining the biomaRt attribute to be
used to define the symbol to be used for each feature (which appears as the
|
feature_id |
character string defining the biomaRt attribute to be used
to define the ID to be used for each feature (which appears as the
|
biomart |
character string defining the biomaRt to be used. Default is
|
dataset |
character string defining the biomaRt dataset to use. Default
is |
host |
optional character string argument which can be used to select a
particular |
See the documentation for the biomaRt package, specifically for the
functions useMart
and getBM
, for information on what are
permitted values for the filters, attributes, biomart, dataset and host
arguments.
a SingleCellExperiment object
## Not run: object <- getBMFeatureAnnos(object) ## End(Not run)