intansv: error reading delly output into R
0
0
Entering edit mode
@abhishek-pratap-4927
Last seen 5.4 years ago
United States

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}

delly SV intansv • 1.0k views
ADD COMMENT
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 326 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6