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Question: ChIPpeakAnno binOverGene error
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gravatar for wuzefeng2008
9 months ago by
wuzefeng20080 wrote:
d<-binOverGene(cvglist,tr,upstream.cutoff =1000,downstream.cutoff = 1000)

 

ERROR: subscript contains out-of-bounds ranges
ADD COMMENTlink modified 9 months ago by Ou, Jianhong1.1k • written 9 months ago by wuzefeng20080
1
gravatar for Ou, Jianhong
9 months ago by
Ou, Jianhong1.1k
United States
Ou, Jianhong1.1k wrote:

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. 

 

ADD COMMENTlink written 9 months ago by Ou, Jianhong1.1k
0
gravatar for Julie Zhu
9 months ago by
Julie Zhu3.8k
United States
Julie Zhu3.8k wrote:

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

ADD COMMENTlink written 9 months ago by Julie Zhu3.8k
0
gravatar for wuzefeng2008
9 months ago by
wuzefeng20080 wrote:

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      
ADD COMMENTlink written 9 months ago by wuzefeng20080
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
ADD REPLYlink written 9 months ago by Julie Zhu3.8k
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