Convert GeneIDs between organisms
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Character vector of GeneIDs, from the species specified by
Name of the current species
Name of the alternate species, to convert the GeneIDs to
a filename or a data.frame
Uses a data frame object of curated GeneIDs. Orthologs are currated from PlasmoDB, OrthoMCL, and other sources.
ortholog(), a character vector of the same length as
genes, holding the one best
GeneID in the other species for each given gene. Genes with no ortholog, and genes not found in
from species, are returned as empty strings.
allOrtholog(), a list of the same length as
genes, holding a vector of
all GeneIDs in all other species, for each given gene. Genes with no ortholog in
any other species are returned as empty vectors.
orthologSet(), a character vector of all found orthologs to any of the given genes. Note that
since orthologs are not in general a one-to-one matching, the returned vector may be longer or shorter than
the input vector of genes.
In general, the set of returned orthologs are not guaranteed to be in the gene annotation of the
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