Links for a list of genes

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Description

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

Usage

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  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

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