[BioC] build BPMAP File

[Kasper Daniel Hansen]

Assuming that chr1 is the first sequence in yopur bpmap file (beware,  
sometimes the first sequences are spike-in controls), it should be as  
simple as

bpmap = readBpmap(FILE)
writeTpmap(filename = "tmp.tpmap", bpmaplist = bpmap[1]) # note just  
single [ so you geta list with one component
tpmap2bpmap(tmpmapname = "tmp.tpmap", bpmapname = "tmp.bpmap")

tpmap2bpmap converts from a text based bpmap file (which according to  
Affy's documentation is called a tpmap file, but I have never seen  
that term used outside of their documentation) into a binary bpmap. In  
case you wonder "tpmap" = "text probe map" and bpmap = "binary probe  
map"

Kasper




On Dec 4, 2008, at 16:48 , Mark Robinson wrote:

> Hi Arnaud.
>
> I suspect the 'writeTpmap' and 'tpmap2bpmap' functions in the  
> 'affxparser' package would be useful for this, though I haven't done  
> it myself ...
>
> > library(affxparser)
> > ?tpmap2bpmap
> > ?writeTpmap
>
> You can use 'readBpmap' to read in your original BPMAP file into a  
> list.
>
> HTH.
> Mark
>
> On 05/12/2008, at 7:56 AM, Droit Arnaud wrote:
>
>> Hello all,
>>
>> I have a BPMAP file (89 Mo) and the size is too big for the  
>> bioconductor’s guideline. I have some alternative as to create a  
>> separate package for the data.
>> But, first, I am thinking to reduce the size of the file by  
>> removing data from the BPMAP file.
>> I want to extract data from BPMAP file (e.g. all data for chr1) and  
>> rebuild BPMAP file with only data from chr1,
>> and I am just wondering if anyone knows if it is possible to  
>> rebuild BPMAP files.
>>
>> Thank you
>>
>> Arnaud Droit.
>>
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>
> ------------------------------
> Mark Robinson
> Epigenetics Laboratory, Garvan
> Bioinformatics Division, WEHI
> e: m.robinson at garvan.org.au
> e: mrobinson at wehi.edu.au
> p: +61 (0)3 9345 2628
> f: +61 (0)3 9347 0852
>
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