link.siggenes {siggenes} | R Documentation |
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, ll = TRUE, refseq = TRUE, symbol = TRUE, omim = TRUE, ug =TRUE, chipname = "", cdfname = NULL, n.digits = 3, title = NULL, bg.col = "white", text.col = "black", link.col = "blue", tableborder = 1, new.window = 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 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(data, cl, ...) |
addDataFrame |
logical indicating if gene-specific information on the differentially expressed genes should be added to the output |
ll |
logical indicating if Entrez/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 |
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 |
Holger Schwender, holger.schw@gmx.de
sam
, ebam
, link.genes
, sam2html
,
ebam2html