[BioC] xmapcore get intronic sequence

Stephen Taylor stephen.taylor at imm.ox.ac.uk
Wed Jul 28 16:39:52 CEST 2010


Hi Tim,


> No, we currently only store the sequence information for exons

Fair enough...

>
> However, I have a site which should allow you to look up that information:
>
> http://xmap.picr.man.ac.uk/sequence/
>
> You should be able to entr your region of interest, and click "View Below"
>

Thanks. I have a lot of probesetids so I'll probably use BioStrings as Vincent suggested or Bio::Ensembl.

On a related note, if do

probeset.to.exon(probesetids),

then I get less rows returned than the size of the probesetids list, I presume because they don't map to known exons.
Since I want to merge this with an existing dataframe that contains the probesetids and expression values, I really need 
it to return a value (FALSE or NA or something) where there is no match so I can do this merge. Is there a way of doing 
this?

Thanks,

Steve

> Cheers,
>
> Tim
>
> On 28/07/2010 14:25, "Stephen Taylor"<stephen.taylor at imm.ox.ac.uk>  wrote:
>
>> Hi,
>>
>> Is there a method in xmapcore to get part of the sequence of the adjoining
>> intron given an exon id?
>>
>> For example:
>>
>>> exon.details("ENSE00001146308")
>> RangedData with 1 row and 5 value columns across 1 space
>>           space             ranges |       stable_id    strand     phase
>>     <character>           <IRanges>  |<character>  <integer>  <integer>
>> 1          17 [7590695, 7590856] | ENSE00001146308        -1        -1
>>     end_phase
>>     <integer>
>> 1        -1
>>
>>                                        sequence
>>
>>                                     <character>
>> 1
>> GTTTTCCCCTCCCATGTGCTCAAGACTGGCGCTAAAAGTTTTGAGCTTCTCAAAAGTCTAGAGCCACCGTCCAGGGAG
>> CAGGTAGCTGCTGGGCTCCGGGGACACTTTGCGTTCGGGCTGGGAGCGTGCTTTCCACGACGGTGACACGCTTCCCTG
>> GATTGG
>>
>>
>> I'd like to get chr17:7590695-7590863
>>
>> Thanks,
>>
>> Steve
>>
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>



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