[BioC] Off-topic unlisting lists and PubMed

Claire Wilson ClaireWilson at PICR.man.ac.uk
Tue Apr 29 15:49:46 MEST 2003


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 Wilson, PhD
Bioinformatics group  
Paterson Institute for Cancer Research  
Christies Hospital NHS Trust  
Wilmslow Road,  
M20 4BX  
tel: +44 (0)161 446 8218

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