[BioC] pmindex in oligo package

[Benilton Carvalho]

say "TilingFeatureSetObject" is your object, you should be able to get  
X and Y coordinates by:

xy.coord <- getPD(TilingFeatureSetObject) 
[pmindex(TilingFeatureSetObject), c("X", "Y")]

i can't check right now, sorry, but i think there's an (unexposed)  
function that should help you with that:

pmi <- pmindex(TilingFeatureSet)
xy.coord2 <- i2xy(pmi, TilingFeatureSet)

let us know how these go and i'll get back to you ASAP.

b

On Nov 15, 2007, at 3:43 PM, Gayla Olbricht wrote:

> Hello,
>
> I am using the oligo package to work with tiling arrays.
>
> I was wondering if there is a way to either:
>
> 1.  See how the pmindex function in oligo is calculating the indices?
> or
> 2.  Obtain the actual x,y coordinates for each probe?
>
> I found the functions indices2xy and xy2indices in the affy package,  
> but can't seem to find an equivalent function in oligo.
>
> Any advise would be greatly appreciated.  My session info is below,  
> in case it is helpful.
>
> Thanks!
> -Gayla Olbricht
>
> _______________________
>> sessionInfo()
> R version 2.6.0 (2007-10-03)
> x86_64-redhat-linux-gnu
>
> locale:
> LC_CTYPE 
> = 
> en_US 
> .UTF 
> -8 
> ;LC_NUMERIC 
> = 
> C 
> ;LC_TIME 
> = 
> en_US 
> .UTF 
> -8 
> ;LC_COLLATE 
> = 
> en_US 
> .UTF 
> -8 
> ;LC_MONETARY 
> = 
> en_US 
> .UTF 
> -8 
> ;LC_MESSAGES 
> = 
> en_US 
> .UTF 
> -8 
> ;LC_PAPER 
> = 
> en_US 
> .UTF 
> -8 
> ;LC_NAME 
> = 
> C 
> ;LC_ADDRESS 
> =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils      
> datasets
> [8] methods   base
>
> other attached packages:
> [1] pd.at35b.mr.v04_1.0.0 oligo_1.2.1           oligoClasses_1.0.3
> [4] affxparser_1.10.1     AnnotationDbi_1.0.6   preprocessCore_1.0.0
> [7] RSQLite_0.6-3         DBI_0.2-4             Biobase_1.16.1
>
> loaded via a namespace (and not attached):
> [1] rcompgen_0.1-15
>
> 	[[alternative HTML version deleted]]
>
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