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 1.5.16 Index]