annotateBMFeatures: Get feature annotation information from Biomart

In scater: Single-Cell Analysis Toolkit for Gene Expression Data in R

Description

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

Usage

annotateBMFeatures(
  ids,
  biomart = "ENSEMBL_MART_ENSEMBL",
  dataset = "mmusculus_gene_ensembl",
  id.type = "ensembl_gene_id",
  symbol.type,
  attributes = c(id.type, symbol.type, "chromosome_name", "gene_biotype",
    "start_position", "end_position"),
  filters = id.type,
  ...
)

getBMFeatureAnnos(x, ids = rownames(x), ...)

Arguments

ids	A character vector containing feature identifiers.
biomart	String defining the biomaRt to be used, to be passed to useMart.
dataset	String defining the dataset to use, to be passed to useMart.
id.type	String specifying the type of identifier in ids.
symbol.type	String specifying the type of symbol to retrieve. If missing, this is set to "mgi_symbol" if dataset="mmusculus_gene_ensembl", or to "hgnc_symbol" if dataset="hsapiens_gene_ensembl",
attributes	Character vector defining the attributes to pass to getBM.
filters	String defining the type of identifier in ids, to be used as a filter in getBM.
...	For annotateBMFeatures, further named arguments to pass to biomaRt::useMart. For getBMFeatureAnnos, further arguments to pass to annotateBMFeatures.
x	A SingleCellExperiment object.

Details

These functions provide convenient wrappers around biomaRt to quickly obtain annotation in the required format.

Value

For annotateBMFeatures, a DataFrame containing feature annotation, with one row per value in ids.

For getBMFeatureAnnos, x is returned containing the output of annotateBMFeatures appended to its rowData.

Author(s)

Aaron Lun, based on code by Davis McCarthy

Examples

## Not run: 
# Making up Ensembl IDs for demonstration purposes.
mock_id <- paste0("ENSMUSG", sprintf("%011d", seq_len(1000)))
anno <- annotateBMFeatures(ids=mock_id)

## End(Not run)

scater documentation built on Feb. 28, 2021, 2:01 a.m.