[BioC] Converting annotate lists to a matrix

[michael watson (IAH-C)]

Hi

Thanks for that :-)  It was actually an easy and quick way to do the
latter that I was looking for.  I can't just undiscrinately get rid of
all integers if they appear at the end of an id in case there are ids
that have integers at the end and are perfectly valid.  So I am left
faced with writing some kind of loop(), which is what I wanted to avoid
in the first place.

I don't want to annoy anyone, but am I the only person who finds the
lists from bioconductor annotation packages a little unhelpful and hard
to work with?  Every example in the help, the first thing they do is
unlist() the list; so why is it a list in the first place??? 

Thanks
Mick

-----Original Message-----
From: John Zhang [mailto:jzhang at jimmy.harvard.edu] 
Sent: 10 February 2005 13:44
To: michael watson (IAH-C)
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Converting annotate lists to a matrix



>This is kind of an R problem, but on bioconductor data.  For example, I

>have the hu6800PATH environment from the hu6800 annotation package.  
>The example in the help is this:
>
>xx <- as.list(hu6800PATH)
>xx <- xx[!is.na(xx)]
>
>What I actually want is a matrix with two columns, the first being 
>probe id and the second being pathway id - I'm going to do some 
>relational joins with this data using merge().

You may try:

> xx <- as.list(hu6800PATH)
> xx <- unlist(xx, use.names = TRUE)
> xx <- cbind(names(xx), xx)

The first column of xx will be probe ids with an integer appended to the
end if 
a probe has multiple mappings. Use pattern match to remove the trailing
integers 
from the first column then you are done.


>
>I've got as far as:
>
>as.matrix(unlist(xx))
>
>But that doesn't give me exactly what I want.  The rownames of the 
>resulting matrix are set to the probe_ids but where there are duplicate

>probe ids (where probes are in >1 pathway) then R appends a numerator 
>on the end.
>
>Can anyone help me convert the list format from an annotation package 
>to a matrix as I describe above?
>
>Thanks
>Mick
>
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Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084