Usage
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)
Arguments
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.