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Question: RiboProfiling Error using countShiftReads function
gravatar for jjblack
22 months ago by
jjblack0 wrote:


I am trying to analyze some Ribo-seq data using the RiboProfiling package. I am attempting to utilize the script attached for analyzing the EFP2 to find pause scores on codon motifs for my own dataset. The script as submitted works with the E. coli data set, but when I try to edit everything for my data, I obtain the following error when using the countShiftReads function:

> countsDataEFP2 <- countShiftReads(exonGRanges[names(cdsPosTransc)], cdsPosTransc,
+                                   alnGRangesEFP2, 9, motifSize=9)​
Error in `colnames<-`(`*tmp*`, value = c("CDS_counts", "fiveUTR_counts",  :
  attempt to set 'colnames' on an object with less than two dimensions

I am using the Saccharomyces cerevisiae GTF from Ensemble converted to a txdb file, and a sorted Bam file for my aligned reads. 

Any assistance as to how to fix this would be very much appreciated.


> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin16.5.0 (64-bit)
Running under: macOS Sierra 10.12.4

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib

[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    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] Rsamtools_1.27.16       RiboProfiling_1.5.3     Biostrings_2.43.8       XVector_0.15.2          GenomicFeatures_1.27.15
 [6] AnnotationDbi_1.37.4    Biobase_2.35.1          GenomicRanges_1.27.23   GenomeInfoDb_1.11.11    IRanges_2.9.19         
[11] S4Vectors_0.13.16       BiocGenerics_0.21.3    

loaded via a namespace (and not attached):
 [1] httr_1.2.1                    AnnotationHub_2.7.17          splines_3.4.0                 gsubfn_0.6-6                 
 [5] shiny_1.0.2                   Formula_1.2-1                 interactiveDisplayBase_1.13.0 latticeExtra_0.6-28          
 [9] RBGL_1.51.0                   BSgenome_1.43.7               GenomeInfoDbData_0.99.0       yaml_2.1.14                  
[13] RSQLite_1.1-2                 backports_1.0.5               lattice_0.20-35               biovizBase_1.23.3            
[17] chron_2.3-50                  digest_0.6.12                 RColorBrewer_1.1-2            checkmate_1.8.2              
[21] colorspace_1.3-2              ggbio_1.23.7                  httpuv_1.3.3                  htmltools_0.3.5              
[25] Matrix_1.2-9                  plyr_1.8.4                    OrganismDbi_1.17.2            XML_3.98-1.6                 
[29] biomaRt_2.31.10               zlibbioc_1.21.0               xtable_1.8-2                  scales_0.4.1                 
[33] BiocParallel_1.9.6            htmlTable_1.9                 tibble_1.3.0                  AnnotationFilter_0.99.8      
[37] ggplot2_2.2.1                 sqldf_0.4-10                  SummarizedExperiment_1.5.9    nnet_7.3-12                  
[41] lazyeval_0.2.0                proto_1.0.0                   mime_0.5                      survival_2.41-3              
[45] magrittr_1.5                  memoise_1.1.0                 GGally_1.3.0                  foreign_0.8-67               
[49] graph_1.53.0                  BiocInstaller_1.25.3          tools_3.4.0                   data.table_1.10.4            
[53] matrixStats_0.52.2            stringr_1.2.0                 munsell_0.4.3                 cluster_2.0.6                
[57] DelayedArray_0.1.11           ensembldb_1.99.14             compiler_3.4.0                grid_3.4.0                   
[61] RCurl_1.95-4.8                dichromat_2.0-0               VariantAnnotation_1.21.19     htmlwidgets_0.8              
[65] labeling_0.3                  bitops_1.0-6                  base64enc_0.1-3               gtable_0.2.0                 
[69] DBI_0.6-1                     reshape_0.8.6                 R6_2.2.0                      reshape2_1.4.2               
[73] GenomicAlignments_1.11.12     gridExtra_2.2.1               knitr_1.15.1                  rtracklayer_1.35.12          
[77] Hmisc_4.0-2                   ProtGenerics_1.7.0            stringi_1.1.5                 Rcpp_0.12.10                 
[81] rpart_4.1-11                  acepack_1.4.1                


riboprofiling • 361 views
ADD COMMENTlink modified 22 months ago • written 22 months ago by jjblack0
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