Runing into error while trying GRanges from R
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Entering edit mode
alva.james • 0
@alvajames-6967
Last seen 3.8 years ago
Germany

Hello All

I have Rdata from bump hunter , I need to proceed with annotation of those results and so  I have started with GRanges

By the following script ,

 regions <- GRanges(seqnames = tab$table$chr, 
+     IRanges(start = tab$table$start, end = tab$table$end),
+     strand = '*', value = tab$table$value, area = tab$table$area, 
+     cluster = tab$table$cluster, L = tab$table$L, clusterL = tab$table$clusterL)


But its throwing me error as,

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘Rle’ for signature ‘"NULL", "missing"

I need to proceed with annotating the resultant *.RData from bumphunter any help is much appreciated.

 sessionInfo()

R version 3.2.1 (2015-06-18)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Ubuntu 14.04.3 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8          LC_NUMERIC=C                 
 [3] LC_TIME=de_DE.UTF-8           LC_COLLATE=en_US.UTF-8       
 [5] LC_MONETARY=de_DE.UTF-8       LC_MESSAGES=en_US.UTF-8      
 [7] LC_PAPER=de_DE.UTF-8          LC_NAME=de_DE.UTF-8          
 [9] LC_ADDRESS=de_DE.UTF-8        LC_TELEPHONE=de_DE.UTF-8     
[11] LC_MEASUREMENT=de_DE.UTF-8    LC_IDENTIFICATION=de_DE.UTF-8

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

other attached packages:
 [1] XLConnect_0.2-12                                  
 [2] XLConnectJars_0.2-12                              
 [3] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1
 [4] minfi_1.16.1                                      
 [5] Biostrings_2.38.4                                 
 [6] XVector_0.10.0                                    
 [7] SummarizedExperiment_1.0.2                        
 [8] lattice_0.20-33                                   
 [9] Biobase_2.30.0                                    
[10] limma_3.26.9                                      
[11] doRNG_1.6                                         
[12] rngtools_1.2.4                                    
[13] pkgmaker_0.22                                     
[14] registry_0.3                                      
[15] doParallel_1.0.10                                 
[16] bumphunter_1.10.0                                 
[17] locfit_1.5-9.1                                    
[18] iterators_1.0.8                                   
[19] foreach_1.4.3                                     
[20] GenomicRanges_1.22.4                              
[21] GenomeInfoDb_1.6.3                                
[22] IRanges_2.4.8                                     
[23] S4Vectors_0.8.11                                  
[24] BiocGenerics_0.16.1                               

loaded via a namespace (and not attached):
 [1] tidyr_0.5.1             nor1mix_1.2-1           splines_3.2.1          
 [4] ellipse_0.3-8           assertthat_0.1          Rsamtools_1.22.0       
 [7] RSQLite_1.0.0           quadprog_1.5-5          digest_0.6.9           
[10] RColorBrewer_1.1-2      colorspace_1.2-6        preprocessCore_1.32.0  
[13] Matrix_1.2-6            plyr_1.8.4              GEOquery_2.36.0        
[16] siggenes_1.44.0         XML_3.98-1.4            mixOmics_6.0.0         
[19] biomaRt_2.26.1          genefilter_1.52.1       zlibbioc_1.16.0        
[22] xtable_1.8-2            corpcor_1.6.8           scales_0.4.0           
[25] BiocParallel_1.4.3      tibble_1.0              openssl_0.9.4          
[28] annotate_1.48.0         beanplot_1.2            ggplot2_2.1.0          
[31] GenomicFeatures_1.22.13 survival_2.39-5         magrittr_1.5           
[34] mclust_5.2              nlme_3.1-128            MASS_7.3-45            
[37] tools_3.2.1             matrixStats_0.50.2      stringr_1.0.0          
[40] munsell_0.4.3           AnnotationDbi_1.32.3    lambda.r_1.1.7         
[43] base64_2.0              compiler_3.2.1          futile.logger_1.4.1    
[46] grid_3.2.1              RCurl_1.95-4.8          igraph_1.0.1           
[49] bitops_1.0-6            gtable_0.2.0            codetools_0.2-14       
[52] multtest_2.26.0         DBI_0.4-1               reshape_0.8.5          
[55] reshape2_1.4.1          R6_2.1.2                illuminaio_0.12.0      
[58] GenomicAlignments_1.6.3 dplyr_0.5.0             rtracklayer_1.30.4     
[61] futile.options_1.0.0    rJava_0.9-8             stringi_1.1.1          
[64] Rcpp_0.12.5             rgl_0.95.1441          
rnaseq bumphunter genomicranges • 674 views
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Entering edit mode

Hi alva.james,

Can you post a head() of the tab dataframe? It will be helpful to get an idea of what is going on here.

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Entering edit mode

Hi,

It's hard for us to help you because:

  1. You're using an unsupported version of Bioconductor. We only support the current version which is BioC 3.3 (requires R 3.3).
  2. You're not providing code that we can reproduce.

H.

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