[BioC] Off-topic unlisting lists and PubMed

Laurent Gautier laurent at cbs.dtu.dk
Tue Apr 29 19:06:27 MEST 2003


I did not follow the tutorials but the following could make the trick.

abstracts <- pm.getabst(genes, "hu6800")

has.word <- unlist(lapply(abstracts, function (x) pm.abstGrep("keyword", x)))


Hopin' it helps,


On Tue, Apr 29, 2003 at 02:49:46PM +0100, Claire Wilson wrote:
> Hi,
> This may seem slightly off topic, but relates to one of the Bioconductor tutorials.  First of all I have list of significant probe ids (say 5).  I then get all the abstracts for these doing:
> 	abstracts <- pm.getabst(genes, "hu6800")
> This gives me a list of length 5 where each entry is a list of objects of class pubMedAbst.  I then identify all abstracts with my keyword of interest in using:
> 	has.word <- sapply(abstracts, function (x) pm.abstGrep("keyword", x))
> which returns a list of length 5, each entry corresponding to a logical vector with the values TRUE or FALSE depending on whether that abstract contained the keyword or not.  Now I want to make a new list that only contains the abstracts with the keyword in it.  Essentially I need to keep all instances of abstracts that correspond to TRUE in has.word.  I have tried many ways of doing this, starting with unlist. Unlist comes back null for abstracts.  I eventually ended up with a bulky, loop construct, but wondered if there was an easier way.
> Many thanks in advance, apologies if this is a bit long winded/directed to the wrong people.
> Claire
> --
> Claire Wilson, PhD
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currently at the National Yang-Ming University in Taipei, Taiwan
Laurent Gautier			CBS, Building 208, DTU
PhD. Student			DK-2800 Lyngby,Denmark	
tel: +45 45 25 24 89		http://www.cbs.dtu.dk/laurent

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