link.genes {siggenes} | R Documentation

## Links for a list of genes

### Description

Generates a htmlpage with links to several public repositories for a list of genes.

### Usage

      link.genes(genenames, filename, entrez = TRUE, refseq = TRUE, symbol = TRUE,
        omim = FALSE, ug = FALSE, fullname = FALSE, which.refseq = "NM",
        chipname = "", cdfname = NULL, refsnp = NULL, max.associated = 2,
        dataframe = NULL, title = NULL, bg.col = "white", text.col = "black",
        link.col = "blue", tableborder = 1, new.window = TRUE, load = TRUE)

### Arguments

`genenames` | a character vector containing the names of the interesting genes.
`filename` | a character string naming the file in which the output should be stored. Must have the suffix ".html".
`entrez` | logical indicating if Entrez links should be added to the output.
`refseq` | logical indicating if RefSeq links should be added to the output.
`symbol` | logical indicating if the gene symbols should be added to the output.
`omim` | logical indicating if OMIM links should be added to the output.
`ug` | logical indicating if UniGene links should be added to the output.
`fullname` | logical indicating whether the full gene names should be added to the output
`which.refseq` | character string or vector naming the first two letters of the RefSeq links that should be displayed in the html file.
`chipname` | character string specifying the chip type used in the analysis. Must be specified as in the metadata section of Bioconductor (e.g., `"hgu133a"` for the Affymetrix HG-U133A chip). Needs not to be specified if `cdfname` is specified. For Affymetrix SNP chips (starting with the 500k array set), `chipname` can be specified by the metadata package name, i.e.\ either by `"pd.genomewidesnp.5"`, by `"pd.genomewidesnp.6"`, by `"pd.mapping250k.nsp"`, or by `"pd.mapping250k.sty"`, to add links to the Affymetrix webpage of the SNPs to the html output.
`cdfname` | character string specifying the cdf name of the used chip. Must exactly follow the nomenclatur of the Affymetrix chips (e.g., `"HG-U133A"` for the Affymetrix HG-U133A chip). If specified, links to the Affymetrix webpage for the interesting genes will be added to the output. If SNP chips are considered, `chipname` instead of `cdfname` must be specified for obtaining these links.
`refsnp` | either a character vector or a data frame. If the former, `refsnp` containis the RefSNP IDs of the SNPs used in the SAM/EBAM analysis, where `names(refsnp)` specifies the names of these SNPs, i.e.\ their probe set IDs. If a data frame, then one column of `refsnp` must contain the RefSNP IDs of the SNPs, and the name of this column must be `RefSNP`. The other columns can contain additional annotations such as the chromosome or the physical position of each SNPs. The row names of `refsnp` must specify the SNPs, i.e.\ must be the probe set IDs of the SNPs. Using `buildSNPannotation` from the package scrime such a data frame can be generated automatically from the metadata package corresponding to the considered SNP chip.
`max.associated` | integer specifying the maximum number of genes associated with the respective SNP displayed in the html output. If all entries should be shown, set `max.associated = 0`. This however might result in a very large html output. For details, see `shortenGeneDescription` in the package scrime.
`dataframe` | data frame having one row for each interesting gene, i.e.\ `nrow(dataframe)` must be equal to `length(genenames)`. The row names of `dataframe` must be equal to `genenames`. This matrix contains additional information on the list of genes that should be added to the output. If `NULL` (default) no information will be added to the link list.
`title` | character string naming the title that should be used in the html page.
`bg.col` | specification of the background color of the html page. See `?par` for how colors can be specified.
`text.col` | specification of the color of the text used in the html page. See `?par` for how colors can be specified.
`link.col` | specification of the color of the links used in the html file. See `?par` for how colors can be specified.
`tableborder` | integer specifying the thickness of the border of the table.
`new.window` | logical indicating if the links should be opened in a new window.
`load` | logical value indicating whether to attempt to load the required annotation data package if it is not already loaded. For details, see the man page of `lookUp` in the package annotate.

### Author(s)

Holger Schwender, holger.schw@gmx.de

### See Also

`SAM-class`, `sam`, `link.siggenes`, `sam2html`

[Package siggenes version 1.64.0 Index]