Hi, I guess I found a little bug in IRanges. When loading a saved RangedData object before loading library(IRanges) before, then IRanges is loaded automatically but the RangeData object is rendered unusable. Only restarting R lets me access the object. The following code reproduces this: $ R --vanilla version 2.11.1 (2010-05-31)... > library(IRanges) > rd = RangedData(IRanges(start=c(1:10), width=2, names=letters[1:10]), space="chr1", score=rnorm(10)) > rd RangedData with 10 rows and 1 value column across 1 space space ranges | score <character> <iranges> | <numeric> a chr1 [ 1, 2] | -0.79949926 b chr1 [ 2, 3] | 1.09152227 c chr1 [ 3, 4] | 0.19032854 d chr1 [ 4, 5] | 0.37248408 e chr1 [ 5, 6] | 0.68396618 f chr1 [ 6, 7] | -1.19804918 g chr1 [ 7, 8] | 0.01221636 h chr1 [ 8, 9] | 0.66203090 i chr1 [ 9, 10] | 0.39848133 j chr1 [10, 11] | 0.15233945 > save(rd, file="rd.r") > q() # restart R $ R --vanilla > load("rd.r") > rd 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 RangedData with 10 rows and 1 column Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent > Note that this depends on presence of rownames. If you make an object rd = RangedData(IRanges(start=c(1:10), width=2), space="chr1", score=rnorm(10)) without named IRanges, the result after loading is > rd 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 RangedData with 10 rows and 1 column chr1 <rangeddata> 1 ######## > sessionInfo() R version 2.11.1 (2010-05-31) 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=no_NO.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=no_NO.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] IRanges_1.6.11 >

Hi Michael -- I think this is a problem in the methods package; the 'show' method found is for DataTable, instead of RangedData. I'll pursue this elsewhere and let you know what comes of it. Martin On 08/13/2010 02:44 AM, Michael Dondrup wrote: > Hi, > I guess I found a little bug in IRanges. When loading a saved RangedData object before loading library(IRanges) > before, then IRanges is loaded automatically but the RangeData object is rendered unusable. Only restarting R lets me access > the object. > The following code reproduces this: > $ R --vanilla > version 2.11.1 (2010-05-31)... >> library(IRanges) >> rd = RangedData(IRanges(start=c(1:10), width=2, names=letters[1:10]), space="chr1", score=rnorm(10)) >> rd > RangedData with 10 rows and 1 value column across 1 space > space ranges | score > <character> <iranges> | <numeric> > a chr1 [ 1, 2] | -0.79949926 > b chr1 [ 2, 3] | 1.09152227 > c chr1 [ 3, 4] | 0.19032854 > d chr1 [ 4, 5] | 0.37248408 > e chr1 [ 5, 6] | 0.68396618 > f chr1 [ 6, 7] | -1.19804918 > g chr1 [ 7, 8] | 0.01221636 > h chr1 [ 8, 9] | 0.66203090 > i chr1 [ 9, 10] | 0.39848133 > j chr1 [10, 11] | 0.15233945 >> save(rd, file="rd.r") >> q() > # restart R > $ R --vanilla >> load("rd.r") >> rd > 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 > > RangedData with 10 rows and 1 column > Error in dimnames(x) <- dn : > length of 'dimnames' [1] not equal to array extent >> > > Note that this depends on presence of rownames. If you make an object > rd = RangedData(IRanges(start=c(1:10), width=2), space="chr1", score=rnorm(10)) > without named IRanges, the result after loading is >> rd > 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 > > RangedData with 10 rows and 1 column > chr1 > <rangeddata> > 1 ######## > >> sessionInfo() > R version 2.11.1 (2010-05-31) > 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=no_NO.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=no_NO.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] IRanges_1.6.11 >> > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793