entrezLinks: Add links to data when using ReportingTools

In jmacdon/affycoretools: Functions useful for those doing repetitive analyses with Affymetrix GeneChips

Add links to data when using ReportingTools

Description

These functions are intended to add links to the Affymetrix, Entrez Gene, Nuccore, and AmiGO databases when creating HTML tables using ReportingTools.

Usage

entrezLinks(df, ...)

Arguments

df	A data.frame, usually created using the select function of the AnnotationDbi package. For Entrez ID data, the column name must be ENTREZID. For Affy data, the column name must be PROBEID, and for GO data the column name must be Term. For Nuccore the column name can be any of "GI", "REFSEQ", "ACCNUM". Any other names will fail.
...	Allows one to pass arbitrary arguments to lower level functions. Currently unsupported.

Details

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.

Value

A data.frame is returned, with links included.

Author(s)

James W. MacDonald [e-mail]

Examples

## 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)

jmacdon/affycoretools documentation built on Nov. 2, 2024, 1:29 a.m.