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
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
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