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, 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")

### Arguments

`object` | A `SingleCellExperiment` object.
`filters` | Character vector defining the filters to pass to the `getBM` function.
`attributes` | Character vector defining the attributes to pass to `getBM`.
`feature_symbol` | String specifying the attribute to be used to define the symbol to be used for each feature Default is `"mgi_symbol"`, using gene symbols for mouse - this should be changed if the organism is not Mus musculus.
`feature_id` | String specifying the attribute to be used to define the ID to be used for each feature. Default is `"ensembl_gene_id"`, using the Ensembl gene IDs.
`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:
    object <- getBMFeatureAnnos(object)

    ## End(Not run)

[Package scater version 1.8.4 Index]