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 |
A |
filters |
Character vector defining the filters to pass to the |
attributes |
Character vector defining the attributes to pass to |
feature_symbol |
String specifying the attribute to be used to define the symbol to be used for each feature
Default is |
feature_id |
String specifying the attribute to be used to define the ID to be used for each feature.
Default is |
biomart |
String defining the biomaRt to be used, to be passed to |
dataset |
String defining the dataset to use, to be passed to |
host |
Character string argument which can be used to select a particular |
A SingleCellExperiment object containing feature annotation.
The input feature_symbol
appears as the feature_symbol
field in the rowData
of the output object.
## Not run: object <- getBMFeatureAnnos(object) ## End(Not run)