getQueryLink {annotate} | R Documentation

## 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 "&nbsp;" 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 <jzhang@jimmy.harvard.edu> with further modifications by James W. MacDonald <jmacdon@med.umich.edu>

[Package annotate version 1.58.0 Index]