Thank you Vince! It works perfectly :)
Just for closure on the topic, I'm adding the code below.
Greetings,
Leonardo
> 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'
> gr2 <- updateObject(gr)
> gr2
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
> 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"
> longGR2 <- updateObject(longGR)
> longGR2
GRanges with 100 ranges and 0 elementMetadata values
seqnames ranges strand |
<Rle> <IRanges> <Rle> |
[1] chr [1, 10] * |
[2] chr [2, 11] * |
[3] chr [3, 12] * |
[4] chr [4, 13] * |
[5] chr [5, 14] * |
[6] chr [6, 15] * |
[7] chr [7, 16] * |
[8] chr [8, 17] * |
[9] chr [9, 18] * |
... ... ... ... ...
[92] chr [ 92, 101] * |
[93] chr [ 93, 102] * |
[94] chr [ 94, 103] * |
[95] chr [ 95, 104] * |
[96] chr [ 96, 105] * |
[97] chr [ 97, 106] * |
[98] chr [ 98, 107] * |
[99] chr [ 99, 108] * |
[100] chr [100, 109] * |
seqlengths
chr
NA
> 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
>
On Wed, Oct 20, 2010 at 8:01 PM, Vincent Carey
<[email protected]>wrote:
> 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
> <[email protected]> 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
> >>
> >
> > [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-sig-sequencing mailing list
> > [email protected]
> > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
> >
>
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