pmAbst2HTML {annotate}R Documentation

HTML Generation for PubMed Abstracts

Description

This function will take a pubMedAbst object, or a list of these objects and generate a simple web page that will list the titles of the abstracts and link to their full page on PubMed

Usage

pmAbst2HTML(absts, filename, title, simple = TRUE, table.center = TRUE)

Arguments

absts A list of pubMedAbst (or a single object)
filename The output filename. Defaults to absts.html
title Extra title information for your listing
simple Whether just to list the title & publication date of the paper or full information. Currently unimplmented.
table.center If TRUE, will center the listing of abstracts

Details

This function uses the Entrez functionality provided by NCBI to retrieve the abstract URL at the PubMed site. It will then create a tabular webpage which will list the titles of the abstracts provided and have them link to the appropriate PubMed page.

Value

A file with the name provided by filename containing a simple HTML file.

Note

The functions are part of Bioconductor project at Dana-Farber Cancer Institute to provide Bioinformatics functionalities through R

Author(s)

Jeff Gentry

See Also

pubMedAbst

Examples

        x <- pubmed("9695952","8325638","8422497")
        a <- xmlRoot(x)
        numAbst <- length(xmlChildren(a))
        absts <- list()
        for (i in 1:numAbst) {
           absts[[i]] <- buildPubMedAbst(a[[i]])
        }
        fname <- tempfile()
        pmAbst2HTML(absts,filename=fname)
        file.remove(fname)

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