[BioC] [devteam-bioc] sort error in GRange

[Valerie Obenchain]

Hi Emily,

We are phasing out the RangedData class for the GRanges class.

You can coerce your RangedData to a GRanges and then sort.

     gr <- as(allorigins, "GRanges")
     sort(gr)

You probably read the BED file in with a function from rtracklayer. In 
the future you can set 'asRangedData=FALSE' and a GRAnges will be 
created instead of a RangedData.

Let me know if you have trouble sorting the GRanges.

Valerie

On 04/30/2013 11:37 AM, Maintainer wrote:
>
> I have chip-seq data, and I would like to use GenomicRanges to count the overlap peaks. The files for the input are BED format generated from the peak calling. I used apply() function to generate bedlist, then I want to combine all those separate GRanges objects, each representing a single bed file, into a single big GRange object. I used do.call() function, then I would like to sort the chromosome location using sort() function, but it gave me an error as below.
>> allorigins=sort(allorigins)
> Error in x[!nas] : selecting spaces: subscript out of bounds
>
> Could you please help me to fix this?
>
> Thanks,
> emily
>
>   -- output of sessionInfo():
>
>> names(bedlist)=NULL
>> allorigins=do.call(c, bedlist)
>> allorigins=sort(allorigins)
> Error in x[!nas] : selecting spaces: subscript out of bounds
>> allorigins
> RangedData with 258508 rows and 1 value column across 240 spaces
>            space                 ranges   |        name
>         <factor>              <IRanges>   | <character>
> 1          chr1     [ 564401,  570399]   |        2726
> 2          chr1     [ 756001,  758799]   |          76
> 3          chr1     [ 811201,  811799]   |          34
> 4          chr1     [ 821801,  826199]   |          43
> 5          chr1     [ 834801,  921999]   |        2607
> 6          chr1     [ 928201,  942399]   |         349
> 7          chr1     [ 944601,  951799]   |          82
> 8          chr1     [ 955801, 1011599]   |        2015
> 9          chr1     [1014001, 1029199]   |         577
> ...         ...                    ... ...         ...
> 258500     chrX [153877201, 153891999]   |        1427
> 258501     chrX [153955401, 153965999]   |         806
> 258502     chrX [154002201, 154014399]   |        1066
> 258503     chrY [  9943601,   9944799]   |         202
> 258504     chrY [  9960801,   9968199]   |         578
> 258505     chrY [  9978601,   9990199]   |        1543
> 258506     chrY [ 10005401,  10010399]   |         502
> 258507     chrY [ 13458601,  13490199]   |       12809
> 258508     chrY [ 59012201,  59020799]   |         902
> Warning messages:
> 1: In `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels) else paste(labels,  :
>    duplicated levels will not be allowed in factors anymore
> 2: In `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels) else paste(labels,  :
>    duplicated levels will not be allowed in factors anymore
>> dim(allorigins)
> [1] 258508      1
>> allorigins[1:5,]
> RangedData with 5 rows and 1 value column across 240 spaces
>       space           ranges |        name
>    <factor>        <IRanges> | <character>
> 1     chr1 [564401, 570399] |        2726
> 2     chr1 [756001, 758799] |          76
> 3     chr1 [811201, 811799] |          34
> 4     chr1 [821801, 826199] |          43
> 5     chr1 [834801, 921999] |        2607
> Warning message:
> In `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels) else paste(labels,  :
>    duplicated levels will not be allowed in factors anymore
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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