autoTranslate: Attempt to automatically translate a gene list

Description

Given a list of query gene list and a target gene list, the function tries find the homology pairing that matches the query list to the target list. The query list is a short list of genes while the target list is supposed to represent a large number of genes from the target species. The default output will be the largest possible list. If returnAllPossible = TRUE then all possible pairings with any matches are returned. It is possible to limit the search by setting possibleOrigins and possibleTargets. Note that gene symbols of some species are more similar to each other than others. Using this with small gene lists and without providing any possibleOrigins or possibleTargets might return multiple hits, or if returnAllPossible = TRUE a wrong match can be returned.

Usage

autoTranslate(genes, targetGenes, possibleOrigins = NULL,
  possibleTargets = NULL, returnAllPossible = FALSE,
  db = homologene::homologeneData)

Arguments

genes

A list of genes to match the target. Symbols or NCBI ids

targetGenes

The target list. This list is supposed to represent a large number of genes from the target species.

possibleOrigins

Taxonomic identifiers of possible origin species

possibleTargets

Taxonomic identifiers of possible target species

returnAllPossible

if TRUE returns all possible pairings with non zero gene matches. If FALSE (default) returns the best match

Homologene database to use.

Value

A data frame if returnAllPossibe = FALSE and a list of data frames if TRUE