link.siggenes: Links for a SAM or an EBAM object
In siggenes: Multiple Testing using SAM and Efron's Empirical Bayes Approaches

Description Usage Arguments Author(s) See Also

Generates a html page with links to several public repositories for a list of genes called differentially expressed when using a specific Delta value in a SAM or an EBAM analysis.

  link.siggenes(object, delta, filename, gene.names = NULL, addDataFrame = TRUE,
        entrez = TRUE, refseq = TRUE, symbol = TRUE, omim = FALSE, ug = FALSE,
        fullname = FALSE, which.refseq = "NM", chipname = "", cdfname = NULL, 
        refsnp = NULL, max.associated = 2, n.digits = 3, title = NULL, 
        bg.col = "white", text.col = "black", link.col = "blue", tableborder = 1, 
        new.window = TRUE, load = TRUE)

`object`	a SAM or an EBAM object.
`delta`	a numerical value specifying the Delta value.
`filename`	character string naming the file in which the output should be stored. Must have the suffix ".html".
`gene.names`	a character vector of the same length as `object@d` (or `object@z`) containing the names of the genes. Must only be specified if it is not specified in `object`, i.e. if it has not been specified in `sam` (or `ebam`).
`addDataFrame`	logical indicating if gene-specific information on the differentially expressed genes should be added to the output.
`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 meta-data 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.
`n.digits`	integer specifying the number of decimal places used in the output.
`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.