[Bioc-sig-seq] GRanges, failure assigning chromosome lengths
Ivan Gregoretti
ivangreg at gmail.com
Mon Apr 26 21:57:20 CEST 2010
Hi Patrick,
You are correct. The validity check is rejecting the input. The
problem with that is that I have three set, all of them failing perhap
because one or two tags are out of bounds.
This tags are coming straight from the Illumina sequencer. There is
no manipulation. Perhaps it is complaining because the validity check
does not know that Mitochondrial DNA is circular.
Bottom line, anybody attempting to load the data as GRanges from a
high coverage tag set will find this seqlengths() rejection.
Is there any way to override it or should I just refrain from
assigning chromosome lengths? The online vignette does not mention if
there is a switch to the validity check.
Thank you,
Ivan
Ivan Gregoretti, PhD
National Institute of Diabetes and Digestive and Kidney Diseases
National Institutes of Health
5 Memorial Dr, Building 5, Room 205.
Bethesda, MD 20892. USA.
Phone: 1-301-496-1592
Fax: 1-301-496-9878
On Mon, Apr 26, 2010 at 3:42 PM, Patrick Aboyoun <paboyoun at fhcrc.org> wrote:
> Ivan,
> As you probably already realized, the first error you encountered was do to
> a misuse of the seqlengths function since function objects (e.g. BSgenome)
> have no sequence lengths.
>
> # Here is the problem
> seqlengths(Z) <- seqlengths(BSgenome)[names(seqlengths(Z))]
> Error in function (classes, fdef, mtable) :
> unable to find an inherited method for function "seqlengths", for
> signature "function"
>
> The second error is the result of a failed validity check on the modified
> object. All ranges stored in a GRanges object must be between 1 and
> seqlengths(object) if the seqlengths information is non-NAs.
>
> # Here is a second attempt that also fails
> seqlengths(Z) <- seqlengths(Mmusculus)[names(seqlengths(Z))]
> Error in validObject(.Object) :
> invalid class "GRanges" object: slot 'ranges' contains values
> outside of sequence bounds
>
> Compare the results of range(Z), which returns the min start and max end for
> each of the seqnames in Z, and compare it with
> seqlengths(Mmusculus)[names(seqlengths(Z))]. This should provide you with
> some insight as to which ranges are out of bounds. Perhaps your intervals
> are 0-based instead of 1-based?
>
>
> Cheers,
> Patrick
>
>
> On 4/26/10 11:08 AM, Ivan Gregoretti wrote:
>>
>> Hello listers,
>>
>> Is anybody having trouble assigning seqlengths() to a GRanges instance
>> with the new GenomicRanges version?
>>
>>
>> This morning I upgraded my GenomicRanges from 0.0.9 to 0.1.17 and
>> since then I am unable to assign chromosome lengths to any of my tag
>> sets from my Illumina 36 nucleotide sequences.
>>
>> On Friday this worked. Let me show you how it complains now:
>>
>> Z<- import('millionsoftags.bed.gz', 'bed')
>>
>> Z<- as(Z, 'GRanges')
>>
>> class(Z)
>> [1] "GRanges"
>> attr(,"package")
>> [1] "GenomicRanges"
>>
>> Z
>> GRanges with 23293177 ranges and 2 elementMetadata values
>> seqnames ranges strand |
>> <Rle> <IRanges> <Rle> |
>> [1] chr1 [3000506, 3000541] + |
>> [2] chr1 [3001061, 3001096] - |
>> [3] chr1 [3001075, 3001110] - |
>> [4] chr1 [3001098, 3001133] + |
>> [5] chr1 [3001310, 3001345] + |
>> [6] chr1 [3001559, 3001594] + |
>> [7] chr1 [3001603, 3001638] + |
>> [8] chr1 [3001603, 3001638] + |
>> [9] chr1 [3001609, 3001644] - |
>> ... ... ... ... ...
>> [23293169] chrY_random [58402685, 58402720] + |
>> [23293170] chrY_random [58403358, 58403393] + |
>> [23293171] chrY_random [58406154, 58406189] + |
>> [23293172] chrY_random [58411077, 58411112] - |
>> [23293173] chrY_random [58430677, 58430712] + |
>> [23293174] chrY_random [58435117, 58435152] - |
>> [23293175] chrY_random [58472079, 58472114] + |
>> [23293176] chrY_random [58483725, 58483760] - |
>> [23293177] chrY_random [58487952, 58487987] - |
>> name score
>> <character> <numeric>
>> [1] HWI-EAS179_1:7:39:506:1302 96
>> [2] HWI-EAS179_1:2:69:562:1539 119
>> [3] HWI-EAS179_1:8:28:1327:394 119
>> [4] HWI-EAS179_1:7:96:619:454 119
>> [5] HWI-EAS179_49:3:4:1219:1729 119
>> [6] HWI-EAS179_49:3:88:949:558 118
>> [7] HWI-EAS179_1:7:60:1151:1790 119
>> [8] HWI-EAS179_1:7:61:1586:147 114
>> [9] HWI-EAS179_1:7:55:813:365 106
>> ... ... ...
>> [23293169] HWI-EAS179_1:7:49:1416:1573 17
>> [23293170] HWI-EAS179_1:8:25:405:1723 59
>> [23293171] HWI-EAS179_1:7:75:1366:1224 25
>> [23293172] HWI-EAS179_1:2:5:1338:80 5
>> [23293173] HWI-EAS179_49:3:13:151:166 83
>> [23293174] HWI-EAS179_49:3:29:1091:472 6
>> [23293175] HWI-EAS179_1:2:69:1424:733 17
>> [23293176] HWI-EAS179_1:7:16:945:1051 25
>> [23293177] HWI-EAS179_1:7:74:1117:1801 14
>>
>> seqlengths
>> chr1 chr10 chr11 ... chrY chrY_random
>> NA NA NA ... NA NA
>>
>> # Here is the problem
>> seqlengths(Z)<- seqlengths(BSgenome)[names(seqlengths(Z))]
>> Error in function (classes, fdef, mtable) :
>> unable to find an inherited method for function "seqlengths", for
>> signature "function"
>>
>> # Here is a second attempt that also fails
>> seqlengths(Z)<- seqlengths(Mmusculus)[names(seqlengths(Z))]
>> Error in validObject(.Object) :
>> invalid class "GRanges" object: slot 'ranges' contains values
>> outside of sequence bounds
>>
>>
>> As you can see, I haven't had the chance to mess the data.
>> Any idea how to circumvent this problem?
>>
>> Thank you,
>>
>> Ivan
>>
>>
>> sessionInfo()
>> R version 2.12.0 Under development (unstable) (2010-03-25 r51410)
>> x86_64-unknown-linux-gnu
>>
>> 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=C 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] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] BSgenome.Mmusculus.UCSC.mm9_1.3.16 BSgenome_1.15.21
>> [3] Biostrings_2.15.27 GenomicRanges_0.1.17
>> [5] IRanges_1.5.79 rtracklayer_1.7.12
>> [7] RCurl_1.4-1 bitops_1.0-4.1
>>
>> loaded via a namespace (and not attached):
>> [1] Biobase_2.7.6 tools_2.12.0 XML_2.8-1
>>
>>
>> Ivan Gregoretti, PhD
>> National Institute of Diabetes and Digestive and Kidney Diseases
>> National Institutes of Health
>>
>> _______________________________________________
>> Bioc-sig-sequencing mailing list
>> Bioc-sig-sequencing at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>
>
>
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