Michael Lawrence | 24 Dec 12:53 2013

Re: RleList

You need RleList(x, compress=FALSE) for cases when sum(elementLengths(x))
exceeds 2^32. The default value of that argument was changed to TRUE last
release cycle.

Michael

On Tue, Dec 24, 2013 at 2:59 AM, Massimo Petretich <petretic@...> wrote:

> Dear All,
>
> I am a hard time converting a list of Rle to a RleList.
> The very same code was working fine with R 2.15.2 and IRanges 1.17.1.
>
>
>
>  BAM<-readAligned(dirPath=directory, pattern=paste("srtRmdup_",tag,
>> ".bam",sep=""), type="BAM")
>>
>
>  lc <- BAM[ !is.na(chromosome(BAM))]
>>
>
>  cvg <- coverage(lc, extend=eval(parse(text=paste(fragmentSize,"L",
>> sep="")))-width(lc))
>>
>
>  y<-mclapply(cvg[sapply(cvg, length)>3*window], smoothRle, window=window,
>> resolution=resolution, mc.cores=cores)
>>
>
>  head(y,2)
>>
> $chr1
> numeric-Rle of length 197195000 with 191252 runs
>   Lengths:          2990000             1000 ...            10000
>   Values :                0 35.7142857142857 ... 1068.71428571429
>
> $chr2
> numeric-Rle of length 181748000 with 178193 runs
>   Lengths:          2990000             1000 ...            11000
>   Values :                0 15.3809523809524 ... 1286.85714285714
>
>  y<-RleList(y)
>>
> Error in .Call2("Rle_constructor", values, lengths, check, 0L, PACKAGE =
> "IRanges") :
> integer overflow while summing elements in 'lengths'
>
>
>
> # It gives the same error if I convert an RleList to list and then back to
> RleList:
>
>
>  cvg
>>
> RleList of length 35
> $chr1
> integer-Rle of length 197195057 with 2181706 runs
>   Lengths: 3000467       2      27     221 ...      98      21     400
> 250
>   Values :       0       1       2       3 ...       2       1       0
>   1
>
> $chr2
> integer-Rle of length 181748164 with 2182776 runs
>   Lengths: 3000128     250     549      99 ...      51       9      48
>  54
>   Values :       0       1       0       1 ...       4       3       2
>   1
>
> $chr3
> integer-Rle of length 159599909 with 1760167 runs
>   Lengths: 2999875     250       6     123 ...      22     136     114
> 136
>   Values :       0       1       0       1 ...       0       1       2
>   1
>
> $chr4
> integer-Rle of length 155630246 with 1888170 runs
>   Lengths: 3000290     250     229     250 ...       5      92     111
>  47
>   Values :       0       1       0       1 ...       2       3       2
>   1
>
> $chr5
> integer-Rle of length 152537402 with 1759560 runs
>   Lengths: 2999987     250     490     196 ...       9     133      14
>   8
>   Values :       0       1       0       1 ...       4       3       2
>   1
> ...
> <30 more elements>
>
>
>  cvgLst <- as.list(cvg)
>>
>
>  cvg <- RleList(cvgLst)
>>
> Error in .Call2("Rle_constructor", values, lengths, check, 0L, PACKAGE =
> "IRanges") :
> integer overflow while summing elements in 'lengths'
>
>
> # The problem isn't likely the data itself or the syntax,
>
>> cvg<-RleList(cvgLst[1:10])
>>
>
>  cvg
>>
> RleList of length 10
> $chr1
> integer-Rle of length 197195057 with 2181706 runs
>   Lengths: 3000467       2      27     221 ...      98      21     400
> 250
>   Values :       0       1       2       3 ...       2       1       0
>   1
>
> $chr2
> integer-Rle of length 181748164 with 2182776 runs
>   Lengths: 3000128     250     549      99 ...      51       9      48
>  54
>   Values :       0       1       0       1 ...       4       3       2
>   1
>
> $chr3
> integer-Rle of length 159599909 with 1760167 runs
>   Lengths: 2999875     250       6     123 ...      22     136     114
> 136
>   Values :       0       1       0       1 ...       0       1       2
>   1
>
> $chr4
> integer-Rle of length 155630246 with 1888170 runs
>   Lengths: 3000290     250     229     250 ...       5      92     111
>  47
>   Values :       0       1       0       1 ...       2       3       2
>   1
>
> $chr5
> integer-Rle of length 152537402 with 1759560 runs
>   Lengths: 2999987     250     490     196 ...       9     133      14
>   8
>   Values :       0       1       0       1 ...       4       3       2
>   1
> ...
> <5 more elements>
>
>
>  sessionInfo()
>>
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8        LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8         LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8     LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8        LC_NAME=C
> [9] LC_ADDRESS=C                LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] MALDIquant_1.8       rtracklayer_1.22.0   ShortRead_1.20.0
> [4] Rsamtools_1.14.2     lattice_0.20-24      Biostrings_2.30.1
> [7] GenomicRanges_1.14.4 XVector_0.2.0        IRanges_1.20.6
> [10] BiocGenerics_0.8.0
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.22.0      bitops_1.0-6        BSgenome_1.30.0
> [4] grid_3.0.2          hwriter_1.3         latticeExtra_0.6-26
> [7] RColorBrewer_1.0-5  RCurl_1.95-4.1      stats4_3.0.2
> [10] tools_3.0.2        XML_3.98-1.1        zlibbioc_1.8.0
>
>
>
>
> Perhaps I am unaware of some changes introduced in the latest version of
> IRanges
> that make this operation not possible,
> I hope somebody has some suggestions to give me.
>
> Thanks and best regards,
> Massimo
>
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>

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