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, ll = FALSE, refseq = TRUE, symbol = TRUE,
    omim = TRUE, ug = TRUE, chipname = "", cdfname = NULL, dataframe = NULL,
    title = NULL, bg.col = "white", text.col = "black", link.col = "blue", 
    tableborder = 1, new.window = 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"
ll logical indicating if Locus 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
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). Need not to be specified if cdfname is specified
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
dataframe matrix having one row for each interesting gene, i.e. nrow(dataframe) must be equal to length(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

Author(s)

Holger Schwender, holger.schw@gmx.de

See Also

SAM-class, sam, link.siggenes, sam2html


[Package siggenes version 1.4.0 Index]