ortholog: Gene Orthologs

Description Usage Arguments Details Value Examples

Description

Convert GeneIDs between organisms

Usage

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ortholog(genes, from = "PF3D7", to = "PY17X")
orthologSet(genes, from = "PF3D7", to = "PY17X")
allOrthologs(genes)
orthologTransform( x, from, to = "Pf3D7", geneColumn = "GENE_ID",
		intensityColumn = "RPKM_M", productColumn="PRODUCT",
		symmetricOnly = FALSE, sep = "\t")

Arguments

genes

Character vector of GeneIDs, from the species specified by from

from

Name of the current species

to

Name of the alternate species, to convert the GeneIDs to

x

a filename or a data.frame

Details

Uses a data frame object of curated GeneIDs. Orthologs are currated from PlasmoDB, OrthoMCL, and other sources.

Value

For 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 the from species, are returned as empty strings.

For 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.

For 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 to species.

Examples

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  ortholog( "PF3D7_0102800", from="PF3D7", to="PY17X")
  orthologSet( "PF3D7_0102800", from="PF3D7", to="PY17X")

robertdouglasmorrison/DuffyTools documentation built on Dec. 7, 2018, 8:02 a.m.