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\name{LL2homology}
\alias{LL2homology}
\alias{HGID2homology}
\alias{ACC2homology}
\title{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 All this functionality has been
replaced by inPARANOID packages.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{
\item{llids}{\code{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}
\item{hgid}{\code{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}
\item{accs}{\code{accs} a vector of character strings for a set of
GenBank Accession numbers}
\item{homoPkg}{\code{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)}
}
\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.
}
\value{
Both functions returns a list of sub-lists containing data for
homologous genes in other organisms.
}
\references{\url{https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?=homologene}}
\author{Jianhua Zhang}
\examples{
\dontrun{
## hsahomology is a deprecated package!
if(require("hsahomology")){
llids <- ls(env = hsahomologyLL2HGID)[2:5]
LL2homology("hsahomology", llids)
}
}
}
\keyword{misc}
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