pm.abstGrep {annotate}R Documentation

An interface to grep for PubMed abstracts.

Description

A user friendly interface to the functionality provided by pubmed.

Usage

pm.abstGrep(pattern, absts, ...)

Arguments

pattern A pattern for the call to grep.
absts A list containing abstracts downloaded using pubmed or equivalent.
... Extra arguments passed to grep.

Details

The absts are a list of PubMed XML objects that have been downloaded and parsed. This function lets the user quickly search the abstracts for any regular expression. The returned value is a logical vector indicating which of the abstracts contain the regular expression.

Value

The returned value is a logical vector indicating which of the abstracts contain the regular expression.

Author(s)

Robert Gentleman

See Also

pm.getabst, pm.titles

Examples

  hoxa9 <- "37809_at"

   ## A bit of a hack to not have a package dependency on hgu95av2
   ## but need to fiddle w/ the warn level to not fail the example anyways.
   curWarn <- getOption("warn")
   options(warn=0)
   on.exit(options(warn=curWarn), add=TRUE)
  if( require(hgu95av2) ) {
     absts <- pm.getabst(hoxa9, "hgu95av2")

     pm.abstGrep("NUP98", absts[[1]])

     pm.abstGrep("apoptosis", absts[[1]])
  }


[Package annotate version 1.8.0 Index]