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, 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 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 |
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. See buildSNPannotation for an automatical way to construct
such a data frame given the corresponding metadata package |
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 |
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 |
Holger Schwender, holger.schw@gmx.de
sam
, ebam
, link.genes
, sam2html
,
ebam2html