\HeaderA{getQueryLink}{Functions to create hypertext links that can be placed in a table
cell of a HTML file}{getQueryLink}
\aliasA{getCells}{getQueryLink}{getCells}
\aliasA{getQuery4Affy}{getQueryLink}{getQuery4Affy}
\aliasA{getQuery4EN}{getQueryLink}{getQuery4EN}
\aliasA{getQuery4FB}{getQueryLink}{getQuery4FB}
\aliasA{getQuery4GB}{getQueryLink}{getQuery4GB}
\aliasA{getQuery4LL}{getQueryLink}{getQuery4LL}
\aliasA{getQuery4OMIM}{getQueryLink}{getQuery4OMIM}
\aliasA{getQuery4SP}{getQueryLink}{getQuery4SP}
\aliasA{getQuery4UG}{getQueryLink}{getQuery4UG}
\aliasA{getTDRows}{getQueryLink}{getTDRows}
\keyword{manip}{getQueryLink}
\begin{Description}\relax
Given a vector of ids, the functions will create a vector of
hypertext links to a defined public repositories such as
LocusLink, UniGene .... The linkages can be placed in a html file
constructed by \code{\LinkA{htmlpage}{htmlpage}}
\end{Description}
\begin{Usage}
\begin{verbatim}
getQueryLink(ids, repository = "ug")
getTDRows(ids, repository = "ug")
getCells(ids, repository = "ug")
getQuery4LL(ids)
getQuery4UG(ids)
getQuery4SP(ids)
getQuery4GB(ids)
getQuery4OMIM(ids)
getQuery4Affy(ids)
getQuery4FB(ids)
getQuery4EN(ids)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{ids}] A character vector of ids, or alternatively, a list
containing character vectors of ids. These will be used to construct
hypertext links. A list should be used in cases where there are
multiple ids per gene.
\item[\code{repository}] A character string for the name of a public
repository. Valid values include "ll", "ug", "gb", "sp", "omim",
"affy", "en", and "fb". 
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
\code{\LinkA{getQuery4LL}{getQuery4LL}} constructs hypertext links to LocusLink using the
provided ids.

\code{\LinkA{getQuery4GB}{getQuery4GB}} constructs hypertext links to GenBank using the
provided ids.

\code{\LinkA{getQuery4UG}{getQuery4UG}} constructs hypertext links to UniGene using the
provided ids.

\code{\LinkA{getQuery4Affy}{getQuery4Affy}} constructs hypertext links to Affymetrix using the
provided ids.

\code{\LinkA{getQuery4SP}{getQuery4SP}} constructs hypertext links to SwissProt using the
provided ids.

\code{\LinkA{getQuery4OMIM}{getQuery4OMIM}} constructs hypertext links to OMIM using the
provided ids.

\code{\LinkA{getQuery4FB}{getQuery4FB}} constructs hypertext links to FlyBase using
the provided ids.

\code{\LinkA{getQuery4EN}{getQuery4EN}} constructs hypertext links to EntrezGene
using the provided ids. This supercedes \code{getQuery4LL}, as
LocusLink has been deprecated by NCBI.

\code{\LinkA{getQueryLink}{getQueryLink}} directs calls to construct hypertext links using
the provided ids.

\code{\LinkA{getTDRows}{getTDRows}} constructs each row of the resulting table.

\code{\LinkA{getCells}{getCells}} constructs each cell of the resulting table.

Note that some of these functions (\code{getQuery4OMIM},
\code{getQuery4UG}, \code{getQuery4LL}), \code{getQuery4FB} attempt to
return empty cells for ids that don't make sense, rather than broken
links. For the other getQuery4XX functions, the end user must replace
all nonsense ids with "\&nbsp;" in order to have an empty cell.
\end{Details}
\begin{Value}
Returns a vector of character strings representing the hypertext links.
\end{Value}
\begin{Note}\relax
The functions are part of Bioconductor project at Dana-Farber
Cancer Institute to provide Bioinformatics functionalities through
R
\end{Note}
\begin{Author}\relax
Jianhua Zhang <jzhang@jimmy.harvard.edu> with further
modifications by James W. MacDonald <jmacdon@med.umich.edu>
\end{Author}

