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.
autoTranslate(genes, targetGenes, possibleOrigins = NULL, possibleTargets = NULL, returnAllPossible = FALSE, db = homologene::homologeneData)
| 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 |
| db | Homologene database to use. |
A data frame if returnAllPossibe = FALSE and a list of data frames if TRUE