Xiang,
This has to do with the fact that the underlying structure mapping keys
(that is here gene symbols) to values (here EG) is a hash table,
designed for a fast lookup, that considers upper-case and lower-case for
the same letter as different symbols.
The cost for an exhaustive search for all upper-case / lower-case
combinations would be prohibitively high.
You can transform the environment org.Mm.egSYMBOL2EG into a list (with
as.list() ) and use grep() on the names if this appears better to you.
Laurent
On 4/7/10 5:48 AM, xuxiang086 wrote:
Hi Martin,
Thanks for your help. It works. But why mget doesn't have an argument
of ignore.case like grep? I think it is necessary, especially when we
retrieve information using gene symbols, which are from different
databases and in different formats.
Best regards, Xiang
2010-04-07
xuxiang086
发件人： Martin Morgan 发送时间： 2010-04-07 10:47:13 收件人： xuxiang086 抄送：
bioc-sig-sequencing 主题： Re: [Bioc-sig-seq] mget with case-insensitive
keys
On 04/06/2010 06:20 PM, xuxiang086 wrote:
Hi all,
I am using the mget function to retrieve some information from
org.eg.Mm.db, but the keys used by mget function are
case-sensitive. How can I make them case-insensitive? Thanks.
Hi Xiang -- I don't know whether you can. Here is a hack that might
work MGET<- function(x, envir, ..., mapWith=toupper) { keys<-
ls(envir) names(keys)<- mapWith(keys) mget(keys[mapWith(x)], envir,
...) } and then
mget("WN", org.Mm.egSYMBOL2EG)
Error in .checkKeys(value, Rkeys(x), x...@ifnotfound) : value for "WN"
not found
MGET("WN", org.Mm.egSYMBOL2EG)
$wn [1] "22407" I haven't really tested it, and it recalculates the
'keys' map between upper and lower case each time so is not
efficient. I wonder what your use case is? Martin
Best regards,
Xiang
2010-04-07
xuxiang086
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