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Question: Getting error using GenomicRanges::setdiff
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gravatar for rubi
3 months ago by
rubi70
rubi70 wrote:

Hi,

 

I'm trying to use GenomicRanges::setdiff and getting an error:

Error in validObject(.Object) : ))
  invalid class “XIntegerViews” object: undefined class for slot "elementMetadata" ("DataTable_OR_NULL")For example,

exon.df <- data.frame(seqnames=rep("chr1",12),id=c(rep("id1",4),rep("id2",3),rep("id3",5)),
                      start=c(10,20,30,40,100,200,300,1000,2000,3000,4000,5000),
                      end=c(15,25,35,45,150,250,350,1500,2500,3500,4500,5500))

cds.df <- data.frame(seqnames=rep("chr1",9),id=c(rep("id1",3),rep("id2",3),rep("id3",3)),
                      start=c(20,30,40,125,200,305,2250,3000,4000),
                      end=c(25,35,45,150,250,325,2500,3500,4250))

utrs.df <- as.data.frame(GenomicRanges::setdiff(makeGRangesFromDataFrame(exon.df,seqnames.field="seqnames"),
                                                makeGRangesFromDataFrame(cds.df,seqnames.field="seqnames")))


Error in validObject(.Object) :
  invalid class “XIntegerViews” object: undefined class for slot "elementMetadata" ("DataTable_OR_NULL")

> sessionInfo()

R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: /usr/local/R-3.4.1/lib64/R/lib/libRblas.so
LAPACK: /usr/local/R-3.4.1/lib64/R/lib/libRlapack.so

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] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] dplyr_0.5.0          data.table_1.10.4    doParallel_1.0.10
 [4] iterators_1.0.8      foreach_1.4.3        snpEnrichment_1.7.0
 [7] rtracklayer_1.34.2   GenomicRanges_1.26.4 GenomeInfoDb_1.10.3
[10] stringi_1.1.2        Biostrings_2.42.0    XVector_0.14.1
[13] IRanges_2.8.2        S4Vectors_0.12.2     BiocGenerics_0.23.0
[16] BiocInstaller_1.24.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.11               compiler_3.4.1
 [3] plyr_1.8.4                 bitops_1.0-6
 [5] tools_3.4.1                zlibbioc_1.20.0
 [7] tibble_1.2                 gtable_0.2.0
 [9] lattice_0.20-34            Matrix_1.2-7.1
[11] DBI_0.6                    snpStats_1.24.0
[13] grid_3.4.1                 Biobase_2.34.0
[15] R6_2.2.0                   XML_3.98-1.4
[17] survival_2.40-1            BiocParallel_1.10.1
[19] magrittr_1.5               ggplot2_2.2.1
[21] Rsamtools_1.26.1           scales_0.4.1
[23] codetools_0.2-15           GenomicAlignments_1.10.0
[25] splines_3.4.1              assertthat_0.1
[27] SummarizedExperiment_1.4.0 colorspace_1.2-7
[29] RCurl_1.95-4.8             lazyeval_0.2.0
[31] munsell_0.4.3

 
ADD COMMENTlink modified 3 months ago by Michael Lawrence9.8k • written 3 months ago by rubi70
2
gravatar for Michael Lawrence
3 months ago by
United States
Michael Lawrence9.8k wrote:

I'm guessing that you might have to reinstall some packages, like S4Vectors.

ADD COMMENTlink written 3 months ago by Michael Lawrence9.8k

BiocInstaller::biocValid() might help remove some of the guess-work.

ADD REPLYlink written 3 months ago by Martin Morgan ♦♦ 20k

Thanks a lot.

 

This, however, returns also the introns. Is it possible to get only the UTRs or to systematically remove the introns?

ADD REPLYlink written 3 months ago by rubi70

I think you replied to the wrong post. But anyway, sure, you just have to use the range() of the CDSs instead.

ADD REPLYlink written 3 months ago by Michael Lawrence9.8k

Right, sorry about that and thanks a lot for the help.

ADD REPLYlink written 3 months ago by rubi70
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