Hi Joseph,
I cannot reproduce this (but I'm still using R-2.12.0):
> library(GenomicRanges)
> z <- GRanges(seqnames=paste("chr",seq(3), sep=""),
+ ranges=IRanges(start=c(1,300,600), width=50),
+ strand=c("+", "-", "*"))
> strand(z)
'factor' Rle of length 3 with 3 runs
Lengths: 1 1 1
Values : + - *
Levels(3): + - *
> strand(z) <- "*"
>
> z
GRanges with 3 ranges and 0 elementMetadata values
seqnames ranges strand |
<Rle> <IRanges> <Rle> |
[1] chr1 [ 1, 50] * |
[2] chr2 [300, 349] * |
[3] chr3 [600, 649] * |
seqlengths
chr1 chr2 chr3
NA NA NA
> sessionInfo()
R version 2.12.0 (2010-10-15)
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_1.2.3 IRanges_1.8.8
What's puzzling me is all those packages loaded via a namespace
that you get. Could it be that something went wrong with your update
from R-2.12.0 to R-2.12.1? I would suggest you reinstall IRanges and
GenomicRanges from scratch see if that solves the problem (and if
it does, then I would suggest you reinstall all your packages from
scratch).
Cheers,
H.
On 01/17/2011 04:05 PM, Joseph Scandura wrote:
I recently updated BioC to 2.12.1 and now find a new issue when assigning
strand to a GRanges object.
The problem must be something straightforward but I have not been able to track
it down.
################### Example:
z=GRanges(seqnames=paste("chr",seq(3), sep=""), ranges = IRanges(start=c(1,300,600), width=50),
strand=c("+", "-", "*"))
strand(z)
'factor' Rle of length 3 with 3 runs
Lengths: 1 1 1
Values : + - *
Levels(3): + - *
strand(z) = "*" #this used to assign a strand of "*" to all elements in z
Error in x[[name, exact = FALSE]] :
missing '[[' method for Sequence class GRanges
traceback()
10: stop("missing '[[' method for Sequence class ", class(x))
9: x[[name, exact = FALSE]]
8: x[[name, exact = FALSE]]
7: object$call
6: object$call
5: update.default(x, strand = value)
4: update(x, strand = value)
3: update(x, strand = value)
2: `strand<-`(`*tmp*`, value = "*")
1: `strand<-`(`*tmp*`, value = "*")
sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats utils methods base
other attached packages:
[1] GenomicRanges_1.2.3 IRanges_1.8.8 Biobase_2.10.0
loaded via a namespace (and not attached):
[1] annotate_1.28.0 AnnotationDbi_1.12.0
biomaRt_2.6.0
[4] Biostrings_2.18.2 BSgenome_1.18.2
BSgenome.Ecoli.NCBI.20080805_1.3.16
[7] ChIPpeakAnno_1.6.0 DBI_0.2-5
DESeq_1.2.1
[10] gdata_2.8.1 genefilter_1.32.0
geneplotter_1.28.0
[13] GO.db_2.4.5 gplots_2.8.0
graphics_2.12.1
[16] grDevices_2.12.1 grid_2.12.1
gtools_2.6.2
[19] limma_3.6.9 MASS_7.3-9
multtest_2.6.0
[22] org.Hs.eg.db_2.4.6 RColorBrewer_1.0-2
RCurl_1.5-0
[25] RMySQL_0.7-5 RSQLite_0.9-4
splines_2.12.1
[28] survival_2.36-2 tools_2.12.1
XML_3.2-0
[31] xtable_1.5-6
###################
Joe
_______________________________________________
Bioc-sig-sequencing mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: [email protected]
Phone: (206) 667-5791
Fax: (206) 667-1319
_______________________________________________
Bioc-sig-sequencing mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
