getQueryLink {annotate} | R Documentation |
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 htmlpage
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)
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. |
repository |
A character string for the name of a public repository. Valid values include "ll", "ug", "gb", "sp", "omim", "affy", "en", and "fb". |
getQuery4LL
constructs hypertext links to LocusLink using the
provided ids.
getQuery4GB
constructs hypertext links to GenBank using the
provided ids.
getQuery4UG
constructs hypertext links to UniGene using the
provided ids.
getQuery4Affy
constructs hypertext links to Affymetrix using the
provided ids.
getQuery4SP
constructs hypertext links to SwissProt using the
provided ids.
getQuery4OMIM
constructs hypertext links to OMIM using the
provided ids.
getQuery4FB
constructs hypertext links to FlyBase using
the provided ids.
getQuery4EN
constructs hypertext links to EntrezGene
using the provided ids. This supercedes getQuery4LL
, as
LocusLink has been deprecated by NCBI.
getQueryLink
directs calls to construct hypertext links using
the provided ids.
getTDRows
constructs each row of the resulting table.
getCells
constructs each cell of the resulting table.
Note that some of these functions (getQuery4OMIM
,
getQuery4UG
, getQuery4LL
), 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 " " in order to have an empty cell.
Returns a vector of character strings representing the hypertext links.
The functions are part of Bioconductor project at Dana-Farber Cancer Institute to provide Bioinformatics functionalities through R
Jianhua Zhang <jzhang@jimmy.harvard.edu> with further modifications by James W. MacDonald <jmacdon@med.umich.edu>