ChIPpeakAnno binOverGene error
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Wojeff • 0
@wojeff-14309
Last seen 14 months ago
d<-binOverGene(cvglist,tr,upstream.cutoff =1000,downstream.cutoff = 1000)

 

ERROR: subscript contains out-of-bounds ranges
chippeakanno binOverGene • 843 views
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Ou, Jianhong ★ 1.2k
@ou-jianhong-4539
Last seen 11 weeks ago
United States

Dear Wuze,

This is a bug in binOverGene when the accumulated given range for any chromosome is greater than 2^31. I tried to fix the bug in next release build (3.12.3). 

Let me know if you still have trouble in using next release build. 

 

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Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 11 weeks ago
United States

Hi, could you please try with upstream.cutoff = 0, downstream.cutoff = 0? Also could you please provide your R session information by typing sessionInfo()? Thanks!

 

Best regards,

 

Julie

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Wojeff • 0
@wojeff-14309
Last seen 14 months ago

Yes, if i set upstream.cutoff = 0, downstream.cutoff = 0, it works, but i wanted to show some flanking  regions. 

and here was my sessioninfo:

R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/lapack/liblapack.so.3.0

locale:
 [1] LC_CTYPE=zh_CN.UTF-8       LC_NUMERIC=C               LC_TIME=zh_CN.UTF-8       
 [4] LC_COLLATE=zh_CN.UTF-8     LC_MONETARY=zh_CN.UTF-8    LC_MESSAGES=zh_CN.UTF-8   
 [7] LC_PAPER=zh_CN.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] GenomicFeatures_1.28.5 AnnotationDbi_1.38.2   Biobase_2.36.2         GenomicRanges_1.28.6  
[5] GenomeInfoDb_1.12.3    IRanges_2.10.5         S4Vectors_0.14.7       BiocGenerics_0.22.1   

loaded via a namespace (and not attached):
 [1] httr_1.3.1                    bit64_0.9-7                   AnnotationHub_2.8.3          
 [4] splines_3.4.2                 shiny_1.0.5                   Formula_1.2-2                
 [7] interactiveDisplayBase_1.14.0 latticeExtra_0.6-28           RBGL_1.52.0                  
[10] blob_1.1.0                    BSgenome_1.44.2               GenomeInfoDbData_0.99.0      
[13] Rsamtools_1.28.0              yaml_2.1.14                   RSQLite_2.0                  
[16] backports_1.1.1               lattice_0.20-35               biovizBase_1.24.0            
[19] digest_0.6.12                 RColorBrewer_1.1-2            XVector_0.16.0               
[22] checkmate_1.8.5               colorspace_1.3-2              ggbio_1.24.1                 
[25] httpuv_1.3.5                  htmltools_0.3.6               Matrix_1.2-11                
[28] plyr_1.8.4                    OrganismDbi_1.18.1            XML_3.98-1.9                 
[31] pkgconfig_2.0.1               biomaRt_2.32.1                zlibbioc_1.22.0              
[34] xtable_1.8-2                  scales_0.5.0                  BiocParallel_1.10.1          
[37] htmlTable_1.9                 tibble_1.3.4                  AnnotationFilter_1.0.0       
[40] ggplot2_2.2.1                 SummarizedExperiment_1.6.5    nnet_7.3-12                  
[43] lazyeval_0.2.1                mime_0.5                      survival_2.41-3              
[46] magrittr_1.5                  memoise_1.1.0                 GGally_1.3.2                 
[49] foreign_0.8-69                graph_1.54.0                  BiocInstaller_1.26.1         
[52] tools_3.4.2                   data.table_1.10.4-3           matrixStats_0.52.2           
[55] stringr_1.2.0                 munsell_0.4.3                 cluster_2.0.6                
[58] DelayedArray_0.2.7            ensembldb_2.0.4               Biostrings_2.44.2            
[61] compiler_3.4.2                rlang_0.1.4                   grid_3.4.2                   
[64] RCurl_1.95-4.8                dichromat_2.0-0               VariantAnnotation_1.22.3     
[67] htmlwidgets_0.9               labeling_0.3                  bitops_1.0-6                 
[70] base64enc_0.1-3               gtable_0.2.0                  curl_3.0                     
[73] DBI_0.7                       reshape_0.8.7                 R6_2.2.2                     
[76] reshape2_1.4.2                GenomicAlignments_1.12.2      gridExtra_2.3                
[79] knitr_1.17                    rtracklayer_1.36.6            bit_1.1-12                   
[82] Hmisc_4.0-3                   ProtGenerics_1.8.0            stringi_1.1.6                
[85] Rcpp_0.12.13                  rpart_4.1-11                  acepack_1.4.1      
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Dear Wuze, Thanks for trying to run with the default setting and posting the session information! The current developer Jianhong is working on debugging and will keep you updated. Best regards, Julie On Nov 28, 2017, at 8:22 PM, wuzefeng2008 [bioc] <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> wrote: Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""> User wuzefeng2008<https: support.bioconductor.org="" u="" 14309=""/> wrote Answer: ChIPpeakAnno binOverGene error<https: support.bioconductor.org="" p="" 103412="" #103520="">: Yes, if i set upstream.cutoff = 0, downstream.cutoff = 0, it works, but i wanted to show some flanking regions. and here was my sessioninfo: R version 3.4.2 (2017-09-28) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.5 LTS Matrix products: default BLAS: /usr/lib/openblas-base/libblas.so.3 LAPACK: /usr/lib/lapack/liblapack.so.3.0 locale: [1] LC_CTYPE=zh_CN.UTF-8 LC_NUMERIC=C LC_TIME=zh_CN.UTF-8 [4] LC_COLLATE=zh_CN.UTF-8 LC_MONETARY=zh_CN.UTF-8 LC_MESSAGES=zh_CN.UTF-8 [7] LC_PAPER=zh_CN.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] GenomicFeatures_1.28.5 AnnotationDbi_1.38.2 Biobase_2.36.2 GenomicRanges_1.28.6 [5] GenomeInfoDb_1.12.3 IRanges_2.10.5 S4Vectors_0.14.7 BiocGenerics_0.22.1 loaded via a namespace (and not attached): [1] httr_1.3.1 bit64_0.9-7 AnnotationHub_2.8.3 [4] splines_3.4.2 shiny_1.0.5 Formula_1.2-2 [7] interactiveDisplayBase_1.14.0 latticeExtra_0.6-28 RBGL_1.52.0 [10] blob_1.1.0 BSgenome_1.44.2 GenomeInfoDbData_0.99.0 [13] Rsamtools_1.28.0 yaml_2.1.14 RSQLite_2.0 [16] backports_1.1.1 lattice_0.20-35 biovizBase_1.24.0 [19] digest_0.6.12 RColorBrewer_1.1-2 XVector_0.16.0 [22] checkmate_1.8.5 colorspace_1.3-2 ggbio_1.24.1 [25] httpuv_1.3.5 htmltools_0.3.6 Matrix_1.2-11 [28] plyr_1.8.4 OrganismDbi_1.18.1 XML_3.98-1.9 [31] pkgconfig_2.0.1 biomaRt_2.32.1 zlibbioc_1.22.0 [34] xtable_1.8-2 scales_0.5.0 BiocParallel_1.10.1 [37] htmlTable_1.9 tibble_1.3.4 AnnotationFilter_1.0.0 [40] ggplot2_2.2.1 SummarizedExperiment_1.6.5 nnet_7.3-12 [43] lazyeval_0.2.1 mime_0.5 survival_2.41-3 [46] magrittr_1.5 memoise_1.1.0 GGally_1.3.2 [49] foreign_0.8-69 graph_1.54.0 BiocInstaller_1.26.1 [52] tools_3.4.2 data.table_1.10.4-3 matrixStats_0.52.2 [55] stringr_1.2.0 munsell_0.4.3 cluster_2.0.6 [58] DelayedArray_0.2.7 ensembldb_2.0.4 Biostrings_2.44.2 [61] compiler_3.4.2 rlang_0.1.4 grid_3.4.2 [64] RCurl_1.95-4.8 dichromat_2.0-0 VariantAnnotation_1.22.3 [67] htmlwidgets_0.9 labeling_0.3 bitops_1.0-6 [70] base64enc_0.1-3 gtable_0.2.0 curl_3.0 [73] DBI_0.7 reshape_0.8.7 R6_2.2.2 [76] reshape2_1.4.2 GenomicAlignments_1.12.2 gridExtra_2.3 [79] knitr_1.17 rtracklayer_1.36.6 bit_1.1-12 [82] Hmisc_4.0-3 ProtGenerics_1.8.0 stringi_1.1.6 [85] Rcpp_0.12.13 rpart_4.1-11 acepack_1.4.1 ________________________________ Post tags: chippeakanno, binOverGene You may reply via email or visit A: ChIPpeakAnno binOverGene error
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