Resolve miRNA identifiers to a canonical namespace

Maps a character vector of miRNA feature identifiers — in any of the supported input namespaces — to either the canonical mature miRNA name ("mirna_name") or the primary MIMAT accession ("mimat"). Case-insensitive matching is applied to MIMAT accessions (the MIMAT prefix is treated case-insensitively); mature names and alias strings are matched with trimmed whitespace but otherwise case-sensitive.

Usage

resolve_mirna_aliases(
  features,
  target_namespace = c("mirna_name", "mimat"),
  table = mirna_alias_table(),
  keep_unresolved = TRUE,
  verbose = FALSE
)

Arguments

features

Character vector of feature identifiers (any mixture of MIMAT accessions, mature miRNA names, precursor MI accessions, or alias strings).

target_namespace

One of "mirna_name" (default) or "mimat"; the namespace to resolve to.

table

A data.frame in the format returned by mirna_alias_table. Override this to use a custom or extended alias table.

keep_unresolved

Logical. If TRUE (default), features with no match in table are returned as NA. If FALSE, an error is raised when any feature cannot be resolved.

verbose

Logical. If TRUE, emits a message listing unresolved features. Default FALSE.

Value

Character vector of the same length as features, with each entry resolved to target_namespace or NA (if unresolved and keep_unresolved = TRUE).

References

Kozomara A., Birgaoanu M., Griffiths-Jones S. (2019) miRBase: from microRNA sequences to function. Nucleic Acids Research 47(D1): D155–D162. DOI: doi:10.1093/nar/gky1141

Examples

# Toray MIMAT IDs → canonical names
resolve_mirna_aliases(c("MIMAT0001631", "MIMAT0000418"))
#> [1] "hsa-miR-451a" NA            

# Legacy name → canonical
resolve_mirna_aliases("hsa-miR-451")
#> [1] "hsa-miR-451a"

# Reverse: canonical name → MIMAT
resolve_mirna_aliases("hsa-miR-451a", target_namespace = "mimat")
#> [1] "MIMAT0001631"