getBMFeatureAnnos {scater} | R Documentation

## Get feature annotation information from Biomart

### Description

Use the biomaRt package to add feature annotation information to an `SingleCellExperiment`.

### Usage

    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")

### Arguments

`object` | A SingleCellExperiment object.
`ids` | A character vector containing the identifiers for all rows of `object`, of the same type specified by `filters`.
`filters` | Character vector defining the filters to pass to the `getBM` function.
`attributes` | Character vector defining the attributes to pass to `getBM`.
`biomart` | String defining the biomaRt to be used, to be passed to `useMart`. Default is `"ENSEMBL_MART_ENSEMBL"`.
`dataset` | String defining the dataset to use, to be passed to `useMart`. Default is `"mmusculus_gene_ensembl"`, which should be changed if the organism is not mouse.
`host` | Character string argument which can be used to select a particular `"host"` to pass to `useMart`. Useful for accessing archived versions of biomaRt data. Default is `"www.ensembl.org"`, in which case the current version of the biomaRt (now hosted by Ensembl) is used.

### Value

A SingleCellExperiment object containing feature annotation. The input `feature_symbol` appears as the `feature_symbol` field in the `rowData` of the output object.

### Examples

    ## 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)

[Package scater version 1.12.2 Index]