Body: <p>I am trying to use the following function in R:</p>
  <pre><code>DBR1 &lt;- readDNAStringSet(file = 'DBR1.fasta')
  DBR1.string &lt;- as.character(DBR1)
  RepeatMatchOutput &lt;- motif_detection(seqName = DBR1, chrs = '', start.position = NA,
                                       end.position = NA, motif = 'GAAGAA', nr.mismatch = 0,
                                       reverse.comp = F, print.status =F)
  </code></pre>
  <p>The error message is:</p>
  <blockquote>
  <p>Error in as.vector(x) : no method for coercing this S4 class to a
  vector</p>
  </blockquote>
  <p>I must be missing something.</p>
  <p>-- output of sessionInfo():</p>
  <pre><code>R version 4.1.2 (2021-11-01
  Platform: x86_64-w64-mingw32/x64 (64-bit)
  Running under: Windows 10 x64 (build 19042)
  
  Matrix products: default
  
  locale:
  [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252   
  [3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                           
  [5] LC_TIME=English_United Kingdom.1252    
  
  attached base packages:
  [1] stats4    stats     graphics  grDevices utils     datasets  methods   base     
  
  other attached packages:
   [1] reshape2_1.4.4                    ggplot2_3.3.5                     gquad_2.1-1                      
   [4] ape_5.6-2                         seqinr_4.2-8                      BiocManager_1.30.16              
   [7] stringr_1.4.0                     STRAH_1.0                         BSgenome.Hsapiens.UCSC.hg19_1.4.3
  [10] BSgenome_1.62.0                   rtracklayer_1.54.0                GenomicRanges_1.46.1             
  [13] Biostrings_2.62.0                 GenomeInfoDb_1.30.1               XVector_0.34.0                   
  [16] IRanges_2.28.0                    S4Vectors_0.32.3                  BiocGenerics_0.40.0              
  
  loaded via a namespace (and not attached):
   [1] SummarizedExperiment_1.24.0 lattice_0.20-45             colorspace_2.0-3            vctrs_0.3.8                
   [5] yaml_2.3.5                  utf8_1.2.2                  XML_3.99-0.8                rlang_1.0.2                
   [9] pillar_1.7.0                withr_2.5.0                 glue_1.6.2                  BiocParallel_1.28.3        
  [13] plyr_1.8.6                  matrixStats_0.61.0          GenomeInfoDbData_1.2.7      lifecycle_1.0.1            
  [17] zlibbioc_1.40.0             MatrixGenerics_1.6.0        munsell_0.5.0               gtable_0.3.0               
  [21] restfulr_0.0.13             Biobase_2.54.0              parallel_4.1.2              fansi_1.0.2                
  [25] Rcpp_1.0.8                  scales_1.1.1                DelayedArray_0.20.0         Rsamtools_2.10.0           
  [29] rjson_0.2.21                stringi_1.7.6               BiocIO_1.4.0                grid_4.1.2                 
  [33] ade4_1.7-18                 cli_3.2.0                   tools_4.1.2                 bitops_1.0-7               
  [37] magrittr_2.0.2              RCurl_1.98-1.6              tibble_3.1.6                crayon_1.5.0               
  [41] pkgconfig_2.0.3             MASS_7.3-54                 ellipsis_0.3.2              Matrix_1.3-4               
  [45] R6_2.5.1                    GenomicAlignments_1.30.0    nlme_3.1-153                compiler_4.1.2 
  <span class="math-container">```</span>
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-03-09T00:52:55.933Z
Comments.Text: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Comments.UserDisplayName: Community
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-04-09T23:19:58.007Z
Comments.Text: what library does `motif_detection` come from? It looks like it might be this but hard to say from what you're doing. What type is `DBR1`? Is it what `seqName` is supposed to be? Is `chrs` the expected type?
Comments.UserDisplayName: Maximilian Press
Tags: <r>
Title: Error in as.character.default(new("BSgenome", pkgname = "BSgenome.Hsapiens.UCSC.hg19", : no method for coercing this S4 class to a vector
ThreadText: # Error in as.character.default(new("BSgenome", pkgname = "BSgenome.Hsapiens.UCSC.hg19", : no method for coercing this S4 class to a vector
  
  (Asked by: username_0 on 2022-03-09)
  
  I am trying to use the following function in R:
  
  ```
  DBR1 <- readDNAStringSet(file = 'DBR1.fasta')
  DBR1.string <- as.character(DBR1)
  RepeatMatchOutput <- motif_detection(seqName = DBR1, chrs = '', start.position = NA,
                                       end.position = NA, motif = 'GAAGAA', nr.mismatch = 0,
                                       reverse.comp = F, print.status =F)
  
  ```
  
  The error message is:
  
  > Error in as.vector(x) : no method for coercing this S4 class to a
  > vector
  
  I must be missing something.
  
  -- output of sessionInfo():
  
  ```
  R version 4.1.2 (2021-11-01
  Platform: x86_64-w64-mingw32/x64 (64-bit)
  Running under: Windows 10 x64 (build 19042)
  
  Matrix products: default
  
  locale:
  [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252   
  [3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                           
  [5] LC_TIME=English_United Kingdom.1252    
  
  attached base packages:
  [1] stats4    stats     graphics  grDevices utils     datasets  methods   base     
  
  other attached packages:
   [1] reshape2_1.4.4                    ggplot2_3.3.5                     gquad_2.1-1                      
   [4] ape_5.6-2                         seqinr_4.2-8                      BiocManager_1.30.16              
   [7] stringr_1.4.0                     STRAH_1.0                         BSgenome.Hsapiens.UCSC.hg19_1.4.3
  [10] BSgenome_1.62.0                   rtracklayer_1.54.0                GenomicRanges_1.46.1             
  [13] Biostrings_2.62.0                 GenomeInfoDb_1.30.1               XVector_0.34.0                   
  [16] IRanges_2.28.0                    S4Vectors_0.32.3                  BiocGenerics_0.40.0              
  
  loaded via a namespace (and not attached):
   [1] SummarizedExperiment_1.24.0 lattice_0.20-45             colorspace_2.0-3            vctrs_0.3.8                
   [5] yaml_2.3.5                  utf8_1.2.2                  XML_3.99-0.8                rlang_1.0.2                
   [9] pillar_1.7.0                withr_2.5.0                 glue_1.6.2                  BiocParallel_1.28.3        
  [13] plyr_1.8.6                  matrixStats_0.61.0          GenomeInfoDbData_1.2.7      lifecycle_1.0.1            
  [17] zlibbioc_1.40.0             MatrixGenerics_1.6.0        munsell_0.5.0               gtable_0.3.0               
  [21] restfulr_0.0.13             Biobase_2.54.0              parallel_4.1.2              fansi_1.0.2                
  [25] Rcpp_1.0.8                  scales_1.1.1                DelayedArray_0.20.0         Rsamtools_2.10.0           
  [29] rjson_0.2.21                stringi_1.7.6               BiocIO_1.4.0                grid_4.1.2                 
  [33] ade4_1.7-18                 cli_3.2.0                   tools_4.1.2                 bitops_1.0-7               
  [37] magrittr_2.0.2              RCurl_1.98-1.6              tibble_3.1.6                crayon_1.5.0               
  [41] pkgconfig_2.0.3             MASS_7.3-54                 ellipsis_0.3.2              Matrix_1.3-4               
  [45] R6_2.5.1                    GenomicAlignments_1.30.0    nlme_3.1-153                compiler_4.1.2 
  ```
  
  ```
  
  **Tags:** r
  
  > **Comments:**
  > **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
  > **username_2**: what library does `motif_detection` come from? It looks like it might be this but hard to say from what you're doing. What type is `DBR1`? Is it what `seqName` is supposed to be? Is `chrs` the expected type?  
  
  ---
  
  ## 0 answers
  
  