getTDRows: Functions to create hypertext links that can be placed in a...

In Bioconductor/annotate: Annotation for microarrays

Functions to create hypertext links that can be placed in a table cell of a HTML file

Description

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.

Usage

getQueryLink(ids, repository = "ug", ...)
getTDRows(ids, repository = "ug", ...)
getCells(ids, repository = "ug", ...)
getQuery4UG(ids, ...)
getQuery4SP(ids, ...)
getQuery4GB(ids, ...)
getQuery4OMIM(ids, ...)
getQuery4Affy(ids, ...)
getQuery4FB(ids, ...)
getQuery4EN(ids, ...)
getQuery4TR(ids, ...)
getQuery4ENSEMBL(ids, ...)

Arguments

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". See the details section for more information.
...	Allows end user to pass additional arguments. See details for getQuery4ENSEMBL for more information.

Details

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.

getQuery4TR constructs hypertext links to TAIR using the provided ids.

getQuery4ENSEMBL constructs hypertext links to Ensembl using the provided ids. An additional 'species' argument must be passed to this function via the ... argument to htmlpage. The form of the argument must be e.g., species="Homo_sapiens" for human. Note the capitalized genus and underscore (_) separator.

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, 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.

Also note that creating additional links is quite simple. First, define a new 'getQuery4XX()' function modeled on the existing functions, then add this function to the getQueryLink function.

Value

Returns a vector of character strings representing the hypertext links.

Author(s)

Jianhua Zhang <[e-mail]> with further modifications by James W. MacDonald <[e-mail]>

Bioconductor/annotate documentation built on Feb. 11, 2024, 8:19 p.m.