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Question: intansv: error reading delly output into R
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gravatar for Abhishek Pratap
2.6 years ago by
United States
Abhishek Pratap170 wrote:

Dear Wen

I am getting the following error when I trying to load delly output run together on 20 samples. 

 

delly <- readDelly(dataDir=data_dir, regSizeLowerCutoff=100, 

               regSizeUpperCutoff=10000000, readsSupport=5,

          method="DELLY", pass=TRUE, minMappingQuality=20)

 


error seen:

{quote}

Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : 
  solving row 1: range cannot be determined from the supplied arguments (too many NAs)
In addition: Warning message:
In readDelly(dataDir = data_dir, regSizeLowerCutoff = 100, regSizeUpperCutoff = 1e+07,  :
  NAs introduced by coercion

{quote}


{quote}

R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] intansv_1.9.0        GenomicRanges_1.18.4
 [3] GenomeInfoDb_1.2.4   IRanges_2.0.1       
 [5] S4Vectors_0.4.0      ggbio_1.14.0        
 [7] gridExtra_0.9.1      GGally_0.5.0        
 [9] tidyr_0.2.0          shiny_0.11.1        
[11] ggvis_0.4.1.9000     shinyBS_0.61        
[13] NMF_0.20.5           Biobase_2.26.0      
[15] BiocGenerics_0.12.1  cluster_2.0.1       
[17] rngtools_1.2.4       pkgmaker_0.22       
[19] registry_0.2         doMC_1.3.3          
[21] iterators_1.0.7      foreach_1.4.2       
[23] data.table_1.9.4     ggplot2_1.0.0       
[25] devtools_1.7.0       dplyr_0.4.1.9000    
[27] plyr_1.8.1           gdata_2.13.3        
[29] scales_0.2.4         reshape2_1.4.1      
[31] RCurl_1.95-4.5       bitops_1.0-6        
[33] rCharts_0.4.5        synapseClient_1.8-4 
[35] nplr_0.1-1          

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3         
 [2] AnnotationDbi_1.28.1    
 [3] assertthat_0.1          
 [4] base64enc_0.1-2         
 [5] BatchJobs_1.5           
 [6] BBmisc_1.9              
 [7] BiocParallel_1.0.3      
 [8] biomaRt_2.22.0          
 [9] Biostrings_2.34.1       
[10] biovizBase_1.14.1       
[11] brew_1.0-6              
[12] BSgenome_1.34.1         
[13] checkmate_1.5.1         
[14] chron_2.3-45            
[15] codetools_0.2-10        
[16] colorspace_1.2-4        
[17] compiler_3.1.2          
[18] DBI_0.3.1               
[19] dichromat_2.0-0         
[20] digest_0.6.8            
[21] doParallel_1.0.8        
[22] fail_1.2                
[23] foreign_0.8-62          
[24] Formula_1.2-0           
[25] GenomicAlignments_1.2.1 
[26] GenomicFeatures_1.18.3  
[27] graph_1.44.1            
[28] gridBase_0.4-7          
[29] gtable_0.1.2            
[30] gtools_3.4.1            
[31] Hmisc_3.15-0            
[32] htmltools_0.2.6         
[33] httpuv_1.3.2            
[34] httr_0.6.1              
[35] labeling_0.3            
[36] lattice_0.20-29         
[37] latticeExtra_0.6-26     
[38] lazyeval_0.1.10.9000    
[39] magrittr_1.5            
[40] MASS_7.3-37             
[41] mime_0.2                
[42] munsell_0.4.2           
[43] nnet_7.3-9              
[44] OrganismDbi_1.8.0       
[45] proto_0.3-10            
[46] R6_2.0.1                
[47] RBGL_1.42.0             
[48] RColorBrewer_1.1-2      
[49] Rcpp_0.11.4             
[50] reshape_0.8.5           
[51] rjson_0.2.15            
[52] RJSONIO_1.3-0           
[53] rpart_4.1-9             
[54] Rsamtools_1.18.2        
[55] RSQLite_1.0.0           
[56] rstudio_0.98.1062       
[57] rstudioapi_0.2          
[58] rtracklayer_1.26.2      
[59] sendmailR_1.2-1         
[60] splines_3.1.2           
[61] stringr_0.6.2           
[62] survival_2.37-7         
[63] tools_3.1.2             
[64] VariantAnnotation_1.12.9
[65] whisker_0.3-2           
[66] XML_3.98-1.1            
[67] xtable_1.7-4            
[68] XVector_0.6.0           
[69] yaml_2.1.13             
[70] zlibbioc_1.12.0    

{quote}

ADD COMMENTlink modified 2.6 years ago by Dan Tenenbaum ♦♦ 8.2k • written 2.6 years ago by Abhishek Pratap170

Which version of DELLY did you use? The format of the output of different version of DELLY has changed. See https://github.com/andrewhzau/intansv for more info.

ADD REPLYlink written 2.6 years ago by ywhzau0
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