entrezLinks | R Documentation |
These functions are intended to add links to the Affymetrix, Entrez Gene, Nuccore, and AmiGO databases when creating HTML tables using ReportingTools.
entrezLinks(df, ...)
df |
A data.frame, usually created using the |
... |
Allows one to pass arbitrary arguments to lower level functions. Currently unsupported. |
These functions are not actually intended to be called directly. Instead,
they are used as targets for the .modifyDF argument of the publish
function of ReportingTools. See the example below for more detail.
A data.frame is returned, with links included.
James W. MacDonald jmacdon@u.washington.edu
## Not run: ## say we have an ExpressionSet from HuGene 1.0 ST array dat <- read.celfiles() eset <- rma(dat) ## annotate the ExpressionSet eset <- annotateEset(eset, hugene10sttranscriptcluster.db, columns = c("ENTREZID","ACCNUM","SYMBOL")) ## and fit a model using limma fit <- lmFit(eset, design) fit2 <- eBayes(fit) ## and create an HTML page with links to Affy and Entrez out <- topTable(fit2, coef=2) htab <- HTMLReport("The title","a_short_name") publish(out, htab, .modifyDF = list(affyLinks, entrezLinks, nuccoreLinks)) finish(htab) ## End(Not run)
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