getBMFeatureAnnos {scater} | R Documentation |
Use the biomaRt package to add feature annotation information to an SingleCellExperiment
.
getBMFeatureAnnos(object, ids = rownames(object), filters = "ensembl_gene_id", attributes = c(filters, "mgi_symbol", "chromosome_name", "gene_biotype", "start_position", "end_position"), biomart = "ENSEMBL_MART_ENSEMBL", dataset = "mmusculus_gene_ensembl", host = "www.ensembl.org")
object |
A SingleCellExperiment object. |
ids |
A character vector containing the identifiers for all rows of |
filters |
Character vector defining the filters to pass to the |
attributes |
Character vector defining the attributes to pass to |
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: data("sc_example_counts") data("sc_example_cell_info") example_sce <- SingleCellExperiment( assays = list(counts = sc_example_counts), colData = sc_example_cell_info ) mock_id <- paste0("ENSMUSG", sprintf("%011d", seq_len(nrow(example_sce)))) example_sce <- getBMFeatureAnnos(example_sce, ids=mock_id) ## End(Not run)