Question: Error with FunciSNP
0
gravatar for musomilan
3.6 years ago by
musomilan0
musomilan0 wrote:

I am trying to learn to use the FunciSNP package to find putatively functional SNPs within an enhancer regions of a GWAS locus. So far, I've just tried to run the practice code, that the developers include in the FunciSNP_vignette.pdf. However, I am unable to run the key function due to the following error.

> glioma <- getFSNPs(snp.regions.file=glioma.snp, bio.features.loc=glioma.bio, bio.features.TSS=F);
Error in getFSNPs(snp.regions.file = glioma.snp, bio.features.loc = glioma.bio,  : 
  unused argument (bio.features.TSS = F)

Could anyone help?  It seems that "bio.features.TSS=FALSE" is not recognized.

Thanks a lot!

 

> sessionInfo() 
R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United Kingdom.1252 
[2] LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

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

other attached packages:
 [1] FunciSNP_1.12.0                        
 [2] RSQLite_1.0.0                          
 [3] DBI_0.3.1                              
 [4] FunciSNP.data_1.6.0                    
 [5] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
 [6] GenomicFeatures_1.22.13                
 [7] AnnotationDbi_1.32.3                   
 [8] Biobase_2.30.0                         
 [9] GenomicRanges_1.22.4                   
[10] GenomeInfoDb_1.6.3                     
[11] IRanges_2.4.8                          
[12] S4Vectors_0.8.11                       
[13] BiocGenerics_0.16.1                    
[14] ggplot2_2.1.0                          

loaded via a namespace (and not attached):
 [1] SummarizedExperiment_1.0.2   VariantAnnotation_1.16.4    
 [3] splines_3.2.2                lattice_0.20-33             
 [5] colorspace_1.2-6             htmltools_0.3.5             
 [7] rtracklayer_1.30.4           interactiveDisplayBase_1.8.0
 [9] survival_2.38-3              XML_3.98-1.4                
[11] RBGL_1.46.0                  ensembldb_1.2.2             
[13] BiocParallel_1.4.3           lambda.r_1.1.7              
[15] matrixStats_0.50.1           plyr_1.8.3                  
[17] zlibbioc_1.16.0              Biostrings_2.38.4           
[19] munsell_0.4.3                gtable_0.2.0                
[21] futile.logger_1.4.1          memoise_1.0.0               
[23] biomaRt_2.26.1               httpuv_1.3.3                
[25] BiocInstaller_1.20.1         ChIPpeakAnno_3.4.6          
[27] Rcpp_0.12.4                  xtable_1.8-2                
[29] scales_0.4.0                 BSgenome_1.38.0             
[31] regioneR_1.2.3               limma_3.26.9                
[33] graph_1.48.0                 XVector_0.10.0              
[35] mime_0.4                     Rsamtools_1.22.0            
[37] AnnotationHub_2.2.5          digest_0.6.9                
[39] shiny_0.13.2                 grid_3.2.2                  
[41] tools_3.2.2                  bitops_1.0-6                
[43] snpStats_1.20.0              RCurl_1.95-4.8              
[45] futile.options_1.0.0         GO.db_3.2.2                 
[47] MASS_7.3-43                  Matrix_1.2-2                
[49] reshape_0.8.5                httr_1.1.0                  
[51] R6_2.1.2                     VennDiagram_1.6.16          
[53] GenomicAlignments_1.6.3      multtest_2.26.0      
snp gwastools R • 654 views
ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by musomilan0

Allright, I have realized that the problem here was simply that the argument "built.in.biofeatures" of the function "getFSNPs" was misannotated as "bio.features.TSS" in the vignette and therefore function didn't recognize it. Now, when I run the function with the correct argument, I am getting a different error.

Command:

> glioma <- getFSNPs(snp.regions.file = glioma.snp, bio.features.loc = glioma.bio, built.in.biofeatures = FALSE);

Could anyone help? It seems that I have some problems with connecting to the 1000 Genomes Database perhaps?

> sessionInfo() 
R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United Kingdom.1252 
[2] LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

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

other attached packages:
 [1] nlme_3.1-121                           
 [2] rtracklayer_1.30.4                     
 [3] org.Hs.eg.db_3.2.3                     
 [4] snpStats_1.20.0                        
 [5] Matrix_1.2-4                           
 [6] survival_2.38-3                        
 [7] plyr_1.8.3                             
 [8] VariantAnnotation_1.16.4               
 [9] SummarizedExperiment_1.0.2             
[10] ChIPpeakAnno_3.4.6                     
[11] VennDiagram_1.6.16                     
[12] futile.logger_1.4.1                    
[13] FunciSNP_1.12.0                        
[14] RSQLite_1.0.0                          
[15] DBI_0.3.1                              
[16] FunciSNP.data_1.6.0                    
[17] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[18] GenomicFeatures_1.22.13                
[19] AnnotationDbi_1.32.3                   
[20] Biobase_2.30.0                         
[21] ggplot2_2.1.0                          
[22] Rsamtools_1.22.0                       
[23] Biostrings_2.38.4                      
[24] XVector_0.10.0                         
[25] GenomicRanges_1.22.4                   
[26] GenomeInfoDb_1.6.3                     
[27] IRanges_2.4.8                          
[28] S4Vectors_0.8.11                       
[29] BiocGenerics_0.16.1                    
[30] BiocInstaller_1.20.1 
ADD REPLYlink written 3.6 years ago by musomilan0
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