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` | an `SingleCellExperiment` object
`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 `attributes` argument of `getBM`.
`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_symbol` in rowData(object), subsequently). Default is `"mgi_symbol"`, gene symbols for mouse. This should be changed if the organism is not Mus musculus!
`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 `feature_id` in rowData(object), subsequently). Default is `"ensembl_gene_id"`, Ensembl gene IDs for mouse. This should be changed if the organism is not Mus musculus!
`biomart` | character string defining the biomaRt to be used. Default is `"ENSEMBL_MART_ENSEMBL"`.
`dataset` | character string defining the biomaRt dataset to use. Default is `"mmusculus_gene_ensembl"`, which should be changed if the organism is not the mouse!
`host` | optional character string argument which can be used to select a particular `"host"` from biomaRt to use. 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.

### Details

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.

### Value

a SingleCellExperiment object

### Examples

    ## Not run:
    object <- getBMFeatureAnnos(object)

    ## End(Not run)

[Package scater version 1.6.3 Index]