miRNA.validate.miR.ID: Validate miR ID's

In drmjc/genomics: Genomics related functions.

Description

EXPERIMENTAL: Take a vector of miR ID's, and the formatted miRbase table, and determine the latest miR ID for each supplied miRNA ALGORITHM for each miR id
if miR ID found in miRBase, then no change
else if miR ID ends in -5p or -3p, and there's only one precursor mir and that mir has a miR on the correct arm (5' or 3') then the correct miR is returned.

Usage

  miRNA.validate.miR.ID(miRids, mirbase5p3p,
    dropped.mirs = NULL)

Details

This handles cases where miRBase uses */<> whereas query uses -5p/-3p else if miR ID ends in *, and there's only one precursor mir, and that mir has two miRs, then use the newest miR ID. This usually corresponds to records in miRbase that used to end in */<>, but now end in -5p/-3p else if miR ID is plain (eg miR-131) and there's only one precursor mir, then choose the oldest miR record. If the mir has only one miR then simple. if mir has 2 miRs then choose the oldest one. Historically mir-123 and miR-123 would have been deposited into db when discovered, and later a (usually) secondard (and thus miR-123*) would have been discovered and deposited in db with a higher MIMAT accession.

Author(s)

Mark Cowley, 2009-01-13

drmjc/genomics documentation built on May 15, 2019, 2:22 p.m.