circRNAprofiler - miRNA binding sites
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Terra • 0
@terra-24154
Last seen 7 months ago

I am attempting to find miRNA binding sites for several circRNAs. I have already performed DEG analysis with EdgeR and selected the top 10 circRNAs (to start with) to find miRNA binding sites using circRNAprofiler.

I have my projectCirc directory set up with an other directory with circRNAs_001.txt containing my list of 10 circRNAs. My experiments.txt is also completed.

My circRNAs_001.txt file looks like this:

circRNA_ID  chrom   gene    strand  startUpBSE  endDownBSE  coverage
1   chr4:89330815-89340100  chr4    TEVA9   +   89330815    89340100    4

My experiments.txt file looks like this:

    label   fileName    condition
1   C1  circRNAs_001.txt    A

I have the below code to start with. I am using gencode v31.

library(BiocManager)
library(pracma)
library(circRNAprofiler)

setwd("/miRNA/")
initCircRNAprofiler(projectFolderName = "projectCirc", detectionTools = "other")
setwd("miRNA/projectCirc/")
check <- checkProjectFolder()
gtf <- formatGTF(pathToGTF = "gencode.v31.annotation.gtf")
backSplicedJunctions <- getBackSplicedJunctions(gtf)

Running the last line above, I get the error message (I have also used gencode v19 and get the same error):

> backSplicedJunctions <- getBackSplicedJunctions(gtf)
Error: Can't combine `..1$id` <logical> and `..2$id` <character>.
Run `rlang::last_error()` to see where the error occurred.

I ran rlang::last_error() but couldn't make any sense of it

> rlang::last_error()
<error/vctrs_error_incompatible_type>
Can't combine `..1$id` <logical> and `..2$id` <character>.
Backtrace:
 1. circRNAprofiler::getBackSplicedJunctions(gtf)
 4. vctrs::vec_default_ptype2(...)
 5. vctrs::stop_incompatible_type(...)
 6. vctrs:::stop_incompatible(...)
 7. vctrs:::stop_vctrs(...)
Run `rlang::last_trace()` to see the full context.
> rlang::last_trace()
<error/vctrs_error_incompatible_type>
Can't combine `..1$id` <logical> and `..2$id` <character>.
Backtrace:
    █
 1. ├─circRNAprofiler::getBackSplicedJunctions(gtf)
 2. │ └─dplyr::bind_rows(backSplicedJunctions, backSplicedJunctionsTool)
 3. │   └─vctrs::vec_rbind(!!!dots, .names_to = .id)
 4. └─vctrs::vec_default_ptype2(...)
 5.   └─vctrs::stop_incompatible_type(...)
 6.     └─vctrs:::stop_incompatible(...)
 7.       └─vctrs:::stop_vctrs(...)

From what I understand it can't merge because one is a logical vector (True/False) and the other is a character, however looking at the classes of gtf with sapply(gtf, class) none of the columns are logical. I don't know how to check the class types circRNAs_001.txt. Any help will be appreciated!

The sessionInfo()

sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /apps/intel/Composer/compilers_and_libraries_2020.0.166/linux/mkl/lib/intel64_lin/libmkl_gf_lp64.so

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

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

other attached packages:
 [1] circRNAprofiler_1.0.0                   gwascat_2.18.0                         
 [3] Homo.sapiens_1.3.1                      TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
 [5] org.Hs.eg.db_3.10.0                     GO.db_3.10.0                           
 [7] OrganismDbi_1.28.0                      GenomicFeatures_1.38.2                 
 [9] GenomicRanges_1.38.0                    GenomeInfoDb_1.22.1                    
[11] AnnotationDbi_1.48.0                    IRanges_2.20.2                         
[13] S4Vectors_0.24.4                        Biobase_2.46.0                         
[15] BiocGenerics_0.32.0                     pracma_2.3.0                           
[17] BiocManager_1.30.10                    

loaded via a namespace (and not attached):
  [1] colorspace_1.4-1                  seqinr_3.6-1                      ellipsis_0.3.1                   
  [4] htmlTable_2.0.0                   XVector_0.26.0                    base64enc_0.1-3                  
  [7] rstudioapi_0.11                   bit64_0.9-7                       interactiveDisplayBase_1.24.0    
 [10] R.methodsS3_1.8.0                 splines_3.6.3                     geneplotter_1.64.0               
 [13] knitr_1.29                        ade4_1.7-15                       Formula_1.2-3                    
 [16] Rsamtools_2.2.3                   annotate_1.64.0                   cluster_2.1.0                    
 [19] dbplyr_1.4.4                      R.oo_1.23.0                       png_0.1-7                        
 [22] graph_1.64.0                      shiny_1.5.0                       readr_1.3.1                      
 [25] compiler_3.6.3                    httr_1.4.1                        backports_1.1.8                  
 [28] assertthat_0.2.1                  Matrix_1.2-18                     fastmap_1.0.1                    
 [31] limma_3.42.2                      later_1.1.0.1                     htmltools_0.5.0                  
 [34] prettyunits_1.1.1                 tools_3.6.3                       gtable_0.3.0                     
 [37] glue_1.4.1                        GenomeInfoDbData_1.2.2            reshape2_1.4.4                   
 [40] dplyr_1.0.0                       rappdirs_0.3.1                    Rcpp_1.0.4.6                     
 [43] vctrs_0.3.1                       Biostrings_2.54.0                 rtracklayer_1.46.0               
 [46] xfun_0.15                         stringr_1.4.0                     mime_0.9                         
 [49] lifecycle_0.2.0                   XML_3.99-0.3                      edgeR_3.28.1                     
 [52] AnnotationHub_2.18.0              MASS_7.3-51.5                     zlibbioc_1.32.0                  
 [55] scales_1.1.1                      BSgenome_1.54.0                   hms_0.5.3                        
 [58] promises_1.1.1                    SummarizedExperiment_1.16.1       RBGL_1.62.1                      
 [61] RColorBrewer_1.1-2                yaml_2.2.1                        curl_4.3                         
 [64] memoise_1.1.0                     gridExtra_2.3                     ggplot2_3.3.2                    
 [67] biomaRt_2.42.1                    rpart_4.1-15                      latticeExtra_0.6-29              
 [70] stringi_1.4.6                     RSQLite_2.2.1                     BiocVersion_3.10.1               
 [73] genefilter_1.68.0                 checkmate_2.0.0                   BiocParallel_1.20.1              
 [76] rlang_0.4.6                       pkgconfig_2.0.3                   matrixStats_0.56.0               
 [79] bitops_1.0-6                      lattice_0.20-38                   purrr_0.3.4                      
 [82] GenomicAlignments_1.22.1          htmlwidgets_1.5.1                 bit_1.1-15.2                     
 [85] tidyselect_1.1.0                  BSgenome.Hsapiens.UCSC.hg19_1.4.0 plyr_1.8.6                       
 [88] magrittr_1.5                      DESeq2_1.26.0                     R6_2.4.1                         
 [91] generics_0.0.2                    Hmisc_4.4-1                       DelayedArray_0.12.3              
 [94] DBI_1.1.0                         pillar_1.4.4                      foreign_0.8-75                   
 [97] survival_3.1-8                    RCurl_1.98-1.2                    nnet_7.3-12                      
[100] tibble_3.0.3                      crayon_1.3.4                      BiocFileCache_1.10.2             
[103] jpeg_0.1-8.1                      progress_1.2.2                    locfit_1.5-9.4                   
[106] grid_3.6.3                        data.table_1.12.8                 blob_1.2.1                       
[109] digest_0.6.25                     xtable_1.8-4                      httpuv_1.5.4                     
[112] R.utils_2.9.2                     openssl_1.4.2                     munsell_0.5.0                    
[115] askpass_1.1
circRNA RNA-seq circRNAprofiler • 178 views
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