LL2homology {annotate} | R Documentation |
These functions are DEPRECATED. All this functionality has been replaced by inPARANOID packages. Given a set of LocusLink ids or NCBI HomoloGeneIDs, the functions obtain the homology data and represent them as a list of sub-lists using the homology data package for the organism of interest. A sub-list can be of length 1 or greater depending on whether a LocusLink id can be mapped to one or more HomoloGeneIDs.
LL2homology(homoPkg, llids) HGID2homology(hgid, homoPkg) ACC2homology(accs, homoPkg)
llids |
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hgid |
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accs |
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homoPkg |
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The homology data package has to be installed before executing any of the two functions.
Each sub-list has the following elements:
homoOrg - a named vector of a single character string whose value is the scientific name of the organism and name the numeric code used by NCBI for the organism.
homoLL - an integer for LocusLink id.
homoHGID - an integer for internal HomoloGeneID.
homoACC - a character string for GenBank accession number of the best matching sequence of the organism.
homoType - a single letter for the type of similarity measurement between the homologous genes. homoType can be either B (reciprocal best best between three or more organisms), b (reciprocal best match between two organisms), or c (curated homology relationship between two organisms).
homoPS - a percentage value measured as the percent of identity of base pair alignment between the homologous sequences.
homoURL - a url to the source if the homology relationship is a curated orthology.
Sub-lists with homoType = B or b will not have any value for homoURL and objects with homoType = c will not have any value for homoPS.
Both functions returns a list of sub-lists containing data for homologous genes in other organisms.
Jianhua Zhang
https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?=homologene
## Not run: ## hsahomology is a deprecated package! if(require("hsahomology")){ llids <- ls(env = hsahomologyLL2HGID)[2:5] LL2homology("hsahomology", llids) } ## End(Not run)