R help - Jul 2007 - Interpreting a string as a variable in a column header

This must be a very simple question, but I can't find any information
on it elsewhere, sorry. When extracting information from a list using
column headers, how do I get R to interpret something as a variable
rather than a string? For example:

xx$"YAL002"

works, but this doesn't:

gene <- "YAL002"
xx$gene

neither do

xx$parse(gene)
xx$eval(gene)
xx$eval(parse(gene))

or a variety of other constructions I have tried.

Background: I have a table of information about yeast genes, and I
also have a list of yeast genes and their GO terms (xx) from the YEAST
package that I downloaded. I want to go through all the genes in my
table and look up their GO terms in the list from the YEAST package.
They might not contain exactly the same genes (ideally they should,
but I'd be surprised if they do) and I don't think they're in the
same
order, so I do want to use the column names, but there are a lot of
them so I'm not typing them all out individually. It might be possible
to turn the GO data into something other than a list, but the help
page recommends using xx <- as.list(YEASTGO) and doesn't make any
other suggestions, so I should probably do as I'm told.

Thanks for any help or suggestions of where to look,

Rosa

Use xx[[gene]] instead of xx$gene (the $ is a shorthand for [[ with some
extra magic to be more convenient, the magic is getting in your way, so
go back to the [[ syntax (make sure you double the braces)).

Hope this helps,

-- 
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.snow at intermountainmail.org
(801) 408-8111
 
 
> -----Original Message-----
> From: r-help-bounces at stat.math.ethz.ch 
> [mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of rosa clements
> Sent: Thursday, July 12, 2007 11:39 AM
> To: r-help at stat.math.ethz.ch
> Subject: [R] Interpreting a string as a variable in a column header
> 
> This must be a very simple question, but I can't find any 
> information on it elsewhere, sorry. When extracting 
> information from a list using column headers, how do I get R 
> to interpret something as a variable rather than a string? 
> For example:
> 
> xx$"YAL002"
> 
> works, but this doesn't:
> 
> gene <- "YAL002"
> xx$gene
> 
> neither do
> 
> xx$parse(gene)
> xx$eval(gene)
> xx$eval(parse(gene))
> 
> or a variety of other constructions I have tried.
> 
> Background: I have a table of information about yeast genes, 
> and I also have a list of yeast genes and their GO terms (xx) 
> from the YEAST package that I downloaded. I want to go 
> through all the genes in my table and look up their GO terms 
> in the list from the YEAST package.
> They might not contain exactly the same genes (ideally they 
> should, but I'd be surprised if they do) and I don't think 
> they're in the same order, so I do want to use the column 
> names, but there are a lot of them so I'm not typing them all 
> out individually. It might be possible to turn the GO data 
> into something other than a list, but the help page 
> recommends using xx <- as.list(YEASTGO) and doesn't make any 
> other suggestions, so I should probably do as I'm told.
> 
> Thanks for any help or suggestions of where to look,
> 
> Rosa
> 
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