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Annotate ninetails output data with biomaRt

Source: R/ninetails_annotation.R
annotate_with_biomart.Rd

Retrieves gene-level annotation from Ensembl for transcripts in ninetails output data. This is a convenience wrapper for getBM with built-in organism presets and support for custom mart objects.

Usage

annotate_with_biomart(
  input_data,
  attributes_to_get = c("ensembl_transcript_id", "external_gene_name", "description",
    "transcript_biotype"),
  filters = "ensembl_transcript_id",
  organism = NULL,
  mart_to_use = NULL
)

Arguments

input_data

Data frame. Tabular output of the ninetails pipeline. Must contain a column named ensembl_transcript_id_short.

attributes_to_get

Character vector. Annotation attributes to retrieve from biomaRt. Default: c("ensembl_transcript_id", "external_gene_name", "description", "transcript_biotype").

filters

Character string. Column of the input data frame to match with the target mart. Default: "ensembl_transcript_id".

organism

Character string or NULL. Organism shorthand for built-in mart presets. Currently available:

"athaliana"

Arabidopsis thaliana (Ensembl Plants)

"hsapiens"

Homo sapiens (Ensembl)

"mmusculus"

Mus musculus (Ensembl)

"scerevisiae"

Saccharomyces cerevisiae (Ensembl Fungi)

Mutually exclusive with mart_to_use. Default: NULL.

mart_to_use

Mart object or NULL. A mart object created with useMart or useEnsembl. Mutually exclusive with organism. Default: NULL.

Value

A data frame with the original ninetails output data joined with the retrieved annotation attributes via left join on transcript IDs.

Details

Requires the biomaRt package version >= 2.40.

Exactly one of organism or mart_to_use must be provided. The two arguments are mutually exclusive; if both are declared the function throws an error.

Acknowledgements

Based on PK (smaegol) NanoTail annotate_with_biomart(): https://github.com/LRB-IIMCB/nanotail/. Many thanks to the NanoTail developer for help and kind advice.

See also

merge_nonA_tables for preparing the input, getBM for the underlying biomaRt query, useMart for creating custom mart objects

Examples

if (FALSE) { # \dontrun{

# With built-in organism preset
annot <- ninetails::annotate_with_biomart(
  input_data = merged_nonA_tables,
  organism = "mmusculus"
)

# With custom mart object
mart <- biomaRt::useMart(
  biomart = "ENSEMBL_MART_ENSEMBL",
  dataset = "hsapiens_gene_ensembl"
)
annot <- ninetails::annotate_with_biomart(
  input_data = merged_nonA_tables,
  mart_to_use = mart
)

} # }