[Bioc-sig-seq] Problem with GenomicRanges: GRanges created prior to R 2.12.0 cannot be loaded with R 2.12.0
Vincent Carey
stvjc at channing.harvard.edu
Thu Oct 21 03:01:43 CEST 2010
try updateObject() on the loaded instances. you will have to
reserialize after this. it is unfortunate that many objects may need
reserialization as definitions change, but updateObject() reduces the
pain.
On Wed, Oct 20, 2010 at 8:24 PM, Leonardo Collado Torres
<lcollado at lcg.unam.mx> wrote:
> Dear bioc-sig-sequencing list,
>
> For several steps in our pipeline we've been saving GRanges objects into
> Rdata files, load them later, and move on. Everything has been smooth so
> far, yet with the new R Release and hence new GenomicRanges there is a
> problem related to the print or show methods in GRanges objects.
>
> The error is related to the new 'seqinfo' part of GRanges objects. The help
> page for seqinfo didn't help us find out if there is a way to make 'old'
> GRanges objects print correctly with the new GenomicRanges package.
>
> With small GRanges objects, R prints an error after printing the head of the
> GRanges object. With longer GRanges objects, only the error is printed. My
> guess is that this is related to the show method for GRanges objects.
>
> Ideally for us, 'old' GRanges objects should still print correctly with the
> new GenomicRanges without having to modify them.
>
> Thank you and greetings,
> Leonardo
>
>
> Case 1: small GRanges
>
> Part 1: creating the object in an older version of R (in this case from
> Ubuntu). The GRanges is the one from the first example of the GenomicRanges
> vignette.
>
>> library(GenomicRanges)
> Loading required package: IRanges
>
> Attaching package: 'IRanges'
>
> The following object(s) are masked from 'package:base':
>
> cbind, eval, Map, mapply, order, paste, pmax, pmax.int, pmin,
> pmin.int, rbind, rep.int, table
>
>> gr <- GRanges(seqnames =
> + Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)),
> + ranges =
> + IRanges(1:10, end = 7:16, names = head(letters, 10)),
> + strand =
> + Rle(strand(c("-", "+", "*", "+", "-")),
> + c(1, 2, 2, 3, 2)),
> + score = 1:10,
> + GC = seq(1, 0, length=10))
>> gr
> GRanges with 10 ranges and 2 elementMetadata values
> seqnames ranges strand | score GC
> <Rle> <IRanges> <Rle> | <integer> <numeric>
> a chr1 [ 1, 7] - | 1 1.0000000
> b chr2 [ 2, 8] + | 2 0.8888889
> c chr2 [ 3, 9] + | 3 0.7777778
> d chr2 [ 4, 10] * | 4 0.6666667
> e chr1 [ 5, 11] * | 5 0.5555556
> f chr1 [ 6, 12] + | 6 0.4444444
> g chr3 [ 7, 13] + | 7 0.3333333
> h chr3 [ 8, 14] + | 8 0.2222222
> i chr3 [ 9, 15] - | 9 0.1111111
> j chr3 [10, 16] - | 10 0.0000000
>
> seqlengths
> chr1 chr2 chr3
> NA NA NA
>> save(gr, file="gr.Rdata")
>> sessionInfo()
> R version 2.12.0 Under development (unstable) (2010-09-08 r52880)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
> [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
> [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8
> [7] LC_PAPER=en_US.utf8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] GenomicRanges_1.1.25 IRanges_1.7.34
>>
>
> Part 2:
> Loading the GRanges object with R 2.11.1 (in this case from Windows). In
> this case everything works fine :)
>
>> load("gr.Rdata")
>> gr
> GRanges with 10 ranges and 2 elementMetadata values
> seqnames ranges strand | score GC
> <Rle> <IRanges> <Rle> | <integer> <numeric>
> a chr1 [ 1, 7] - | 1 1.0000000
> b chr2 [ 2, 8] + | 2 0.8888889
> c chr2 [ 3, 9] + | 3 0.7777778
> d chr2 [ 4, 10] * | 4 0.6666667
> e chr1 [ 5, 11] * | 5 0.5555556
> f chr1 [ 6, 12] + | 6 0.4444444
> g chr3 [ 7, 13] + | 7 0.3333333
> h chr3 [ 8, 14] + | 8 0.2222222
> i chr3 [ 9, 15] - | 9 0.1111111
> j chr3 [10, 16] - | 10 0.0000000
>
> seqlengths
> chr1 chr2 chr3
> NA NA NA
>> sessionInfo()
> R version 2.11.1 (2010-05-31)
> x86_64-pc-mingw32
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] GenomicRanges_1.0.6 IRanges_1.6.8
>>
>
>
> Part 3:
> Loading the GRanges object into the new R (2.12.0) pops an error:
>
>> library(GenomicRanges)
> Loading required package: IRanges
>
> Attaching package: 'IRanges'
>
> The following object(s) are masked from 'package:base':
>
> cbind, eval, Map, mapply, order, paste, pmax, pmax.int, pmin,
> pmin.int, rbind, rep.int, table
>
>> load("gr.Rdata")
>> gr
> GRanges with 10 ranges and 2 elementMetadata values
> seqnames ranges strand | score GC
> <Rle> <IRanges> <Rle> | <integer> <numeric>
> a chr1 [ 1, 7] - | 1 1.0000000
> b chr2 [ 2, 8] + | 2 0.8888889
> c chr2 [ 3, 9] + | 3 0.7777778
> d chr2 [ 4, 10] * | 4 0.6666667
> e chr1 [ 5, 11] * | 5 0.5555556
> f chr1 [ 6, 12] + | 6 0.4444444
> g chr3 [ 7, 13] + | 7 0.3333333
> h chr3 [ 8, 14] + | 8 0.2222222
> i chr3 [ 9, 15] - | 9 0.1111111
> j chr3 [10, 16] - | 10 0.0000000
> Error in seqlengths(seqinfo(x)) :
> error in evaluating the argument 'x' in selecting a method for function
> 'seqlengths'
>> sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] GenomicRanges_1.2.0 IRanges_1.8.0
>>
>
>
>
>
>
> Case 2: long GRanges object (longer 21 ranges)
>
> Part 1: Creating the GRanges object in R 2.11.1
>
>> library(GenomicRanges)
> Loading required package: IRanges
>
> Attaching package: 'IRanges'
>
> The following object(s) are masked from 'package:base':
>
> cbind, Map, mapply, order, paste, pmax, pmax.int, pmin, pmin.int,
> rbind, rep.int, table
>
>> longGR <- GRanges(seqnames=rep("chr", 100), ranges=IRanges(start=1:101,
> width=10), strand=rep("*", 100))
> Error in validObject(.Object) :
> invalid class "GRanges" object: slot lengths are not all equal
>> length(1:101)
> [1] 101
>> longGR <- GRanges(seqnames=rep("chr", 100), ranges=IRanges(start=1:100,
> width=10), strand=rep("*", 100))
>>
>>
>> save(longGR, file="longGR.Rdata")
>> sessionInfo()
> R version 2.11.1 (2010-05-31)
> x86_64-pc-mingw32
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] GenomicRanges_1.0.6 IRanges_1.6.8
>>
>
>
> Part 2: loading the file in R 2.12.0 pops an error:
>
>> load("longGR.Rdata")
>> longGR
> GRanges with 100 ranges and 0 elementMetadata values
> Error in validObject(.Object) :
> invalid class "GRanges" object: slots in class definition but not in
> object: "seqinfo"
>> sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] GenomicRanges_1.2.0 IRanges_1.8.0
>>
>
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>
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