annotate (version 1.44.0)

LL2homology: DEPRECATED Functions that find the homology data for a given set of LocusLink ids or HomoloGeneIDs

Description

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 All this functionality has been replaced by inPARANOID packages.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.

Usage

LL2homology(homoPkg, llids)
HGID2homology(hgid, homoPkg)
ACC2homology(accs, homoPkg)

Arguments

llids

llids a vector of character strings or numberic numbers for a set of LocusLink ids whose homologous genes in other organisms are to be found

hgid

hgid a named vector of character strings or numberic numbers for a set of HomoloGeneIDs whose homologous genes in other organisms are to be found. Names of the vector give the code used by NCBI for organisms

accs

accs a vector of character strings for a set of GenBank Accession numbers

homoPkg

homoPkg a character string for the name of the homology data package for a given organism, which is a short version of the scientific name of the organism plus homology (e. g. hsahomology)

Value

Both functions returns a list of sub-lists containing data for homologous genes in other organisms.

Details

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.

References

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?=homologene

Examples

## Not run: 
#     ## hsahomology is a deprecated package! 
#     if(require("hsahomology")){
#         llids <- ls(env = hsahomologyLL2HGID)[2:5]
#         LL2homology("hsahomology", llids)
#     }
#     
# ## End(Not run)