[BioC] pmindex in oligo package

[Benilton Carvalho]

my bad. Because i2xy is not exposed, you need  to do sth like:

idx = oligo:::i2xy(pmi, data_bpmap)
B

On Nov 15, 2007, at 9:36 PM, "Gayla Olbricht" <ghobbs at stat.purdue.edu>  
wrote:

> Hi Benilton,
>
> Thanks for the advice.
>
> So, when I ran the first thing you suggested, I got the following  
> error:
>
>> xy.coord <- getPD(data_bpmap) [pmindex(data_bpmap), c("X", "Y")]
> Error in getPD(data_bpmap)[pmindex(data_bpmap), c("X", "Y")] :
> object is not subsettable
>
> But, was able to use your suggestion as a hint to get at the X,Y  
> coordinates for PM values by the following:
> feature<-getPD(data_bpmap)
> PMxcoord<-feature$X[pmindex(data_bpmap)]
> PMycoord<-feature$Y[pmindex(data_bpmap)]
>
> This seems to give me what I need.
>
> I'm still not exactly sure how the pmindex is calculated, but maybe  
> the x,y coordinate information will be all I need.
>
> I did try running the function i2xy and got the following:
>
>> pmi <- pmindex(data_bpmap)
>> xy.coord2 <- i2xy(pmi, data_bpmap)
> Error: could not find function "i2xy"
>
> The same thing happened when I tried "indices2xy" instead.
>
> I would still be interested to know if the i2xy function can work,  
> but I guess I can do without it since I have the x,y information.
>
> Thanks again for your quick response and help with this!
> -Gayla
>
>
>
>
>
>
>
> ----- Original Message ----- From: "Benilton Carvalho" <bcarvalh at jhsph.edu 
> >
> To: "Gayla Olbricht" <ghobbs at stat.purdue.edu>
> Cc: <bioconductor at stat.math.ethz.ch>
> Sent: Thursday, November 15, 2007 3:56 PM
> Subject: Re: [BioC] pmindex in oligo package
>
>
>> 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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