Question: setting names of GAlignmentsList objects
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gravatar for Hans-Ulrich Klein
6.1 years ago by
United States
Hans-Ulrich Klein330 wrote:
Dear all, I can not change the list element names of my GAlignmentsList objects: library(GenomicRanges) library(Rsamtools) ex1_file <- system.file("extdata", "ex1.bam", package="Rsamtools") ga <- readGappedAlignments(ex1_file) galist <- GAlignmentsList(one=gal, two=gal) names(galist) names(galist) <- c("three", "four") Error in `names<-`(`*tmp*`, value = c("three", "four")) : replacement 'value' is not an AtomicList with the same elementLengths as 'x' names(galist) <- names(galist) Error in `names<-`(`*tmp*`, value = c("one", "two")) : replacement 'value' is not an AtomicList with the same elementLengths as 'x' Any ideas what is going wrong? Thanks and best wishes, Hans > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-pc-linux-gnu (64-bit) 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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] Rsamtools_1.12.4 Biostrings_2.28.0 GenomicRanges_1.12.5 [4] IRanges_1.18.4 BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] bitops_1.0-6 stats4_3.0.1 tools_3.0.1 zlibbioc_1.6.0 -- Dr. Hans-Ulrich Klein Institute of Medical Informatics University of M?nster Albert-Schweitzer-Campus 1 Geb?ude A11 48149 M?nster, Germany Tel.: +49 (0)251 83-58405
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ADD COMMENTlink modified 6.1 years ago by Martin Morgan ♦♦ 24k • written 6.1 years ago by Hans-Ulrich Klein330
Answer: setting names of GAlignmentsList objects
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gravatar for Martin Morgan
6.1 years ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:
On 10/31/2013 02:53 AM, Hans-Ulrich Klein wrote: > Dear all, > > I can not change the list element names of my GAlignmentsList objects: > > library(GenomicRanges) > library(Rsamtools) > ex1_file <- system.file("extdata", "ex1.bam", package="Rsamtools") > ga <- readGappedAlignments(ex1_file) The name of this function was changed to readGAlignments in the current version of Bioconcductor > galist <- GAlignmentsList(one=gal, two=gal) oops, one=ga, two=ga > names(galist) > > names(galist) <- c("three", "four") > Error in `names<-`(`*tmp*`, value = c("three", "four")) : > replacement 'value' is not an AtomicList with the same elementLengths as 'x' > > names(galist) <- names(galist) > Error in `names<-`(`*tmp*`, value = c("one", "two")) : > replacement 'value' is not an AtomicList with the same elementLengths as 'x' this works in the current release; try biocLite("BiocUpgrade") and get (other than the R version) > sessionInfo() R version 3.0.2 Patched (2013-10-02 r64018) Platform: x86_64-unknown-linux-gnu (64-bit) 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=en_US.UTF-8 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] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] Rsamtools_1.14.1 Biostrings_2.30.0 GenomicRanges_1.14.3 [4] XVector_0.2.0 IRanges_1.20.4 BiocGenerics_0.8.0 [7] BiocInstaller_1.12.0 loaded via a namespace (and not attached): [1] bitops_1.0-6 stats4_3.0.2 zlibbioc_1.8.0 > > > Any ideas what is going wrong? > > Thanks and best wishes, > Hans > > > > sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-pc-linux-gnu (64-bit) > > 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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] Rsamtools_1.12.4 Biostrings_2.28.0 GenomicRanges_1.12.5 > [4] IRanges_1.18.4 BiocGenerics_0.6.0 > > loaded via a namespace (and not attached): > [1] bitops_1.0-6 stats4_3.0.1 tools_3.0.1 zlibbioc_1.6.0 > > -- 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
ADD COMMENTlink written 6.1 years ago by Martin Morgan ♦♦ 24k
Dear Martin, yes, it is going nicely in the current release. I pasted the sessionInfo() but did not look at it :/ Sorry. Best, Hans On 31/10/13 12:45, Martin Morgan wrote: > On 10/31/2013 02:53 AM, Hans-Ulrich Klein wrote: >> Dear all, >> >> I can not change the list element names of my GAlignmentsList objects: >> >> library(GenomicRanges) >> library(Rsamtools) >> ex1_file <- system.file("extdata", "ex1.bam", package="Rsamtools") >> ga <- readGappedAlignments(ex1_file) > > The name of this function was changed to readGAlignments in the > current version of Bioconcductor > >> galist <- GAlignmentsList(one=gal, two=gal) > > oops, one=ga, two=ga > >> names(galist) >> >> names(galist) <- c("three", "four") >> Error in `names<-`(`*tmp*`, value = c("three", "four")) : >> replacement 'value' is not an AtomicList with the same >> elementLengths as 'x' >> >> names(galist) <- names(galist) >> Error in `names<-`(`*tmp*`, value = c("one", "two")) : >> replacement 'value' is not an AtomicList with the same >> elementLengths as 'x' > > this works in the current release; try > > biocLite("BiocUpgrade") > > and get (other than the R version) > > > sessionInfo() > R version 3.0.2 Patched (2013-10-02 r64018) > Platform: x86_64-unknown-linux-gnu (64-bit) > > 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=en_US.UTF-8 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] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] Rsamtools_1.14.1 Biostrings_2.30.0 GenomicRanges_1.14.3 > [4] XVector_0.2.0 IRanges_1.20.4 BiocGenerics_0.8.0 > [7] BiocInstaller_1.12.0 > > loaded via a namespace (and not attached): > [1] bitops_1.0-6 stats4_3.0.2 zlibbioc_1.8.0 > >> >> >> Any ideas what is going wrong? >> >> Thanks and best wishes, >> Hans >> >> >> > sessionInfo() >> R version 3.0.1 (2013-05-16) >> Platform: x86_64-pc-linux-gnu (64-bit) >> >> 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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] Rsamtools_1.12.4 Biostrings_2.28.0 GenomicRanges_1.12.5 >> [4] IRanges_1.18.4 BiocGenerics_0.6.0 >> >> loaded via a namespace (and not attached): >> [1] bitops_1.0-6 stats4_3.0.1 tools_3.0.1 zlibbioc_1.6.0 >> >> > > -- Dr. Hans-Ulrich Klein Institute of Medical Informatics University of M?nster Albert-Schweitzer-Campus 1 Geb?ude A11 48149 M?nster, Germany Tel.: +49 (0)251 83-58405
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