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lpantano / isomiRs

analyze isomiRs from seqbuster tool
http://lpantano.github.io/isomiRs/
MIT License
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IsomirDataSeqFromFiles rank error #20

Closed BineStancic closed 2 years ago

BineStancic commented 2 years ago

I ran into an issue when trying to read ".mirna" files using IsomirDataSeqFromFiles.

But I still get the following error in the last step.

> ids <- IsomirDataSeqFromFiles(fn_list, coldata=de)

Error in (function (cond)  :                                                                                       
  error in evaluating the argument 'x' in selecting a method for function 'unique': Problem with `mutate()` column `rank`.
ℹ `rank = 1:n()`.
ℹ `rank` must be size 0 or 1, not 2.

Session info:

R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

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

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

other attached packages:
 [1] isomiRs_1.22.0              SummarizedExperiment_1.24.0
 [3] Biobase_2.54.0              GenomicRanges_1.46.1       
 [5] GenomeInfoDb_1.30.1         IRanges_2.28.0             
 [7] S4Vectors_0.32.3            BiocGenerics_0.40.0        
 [9] MatrixGenerics_1.6.0        matrixStats_0.61.0         
[11] DiscriMiner_0.1-29         

loaded via a namespace (and not attached):
  [1] assertive.base_0.0-9        colorspace_2.0-2           
  [3] rjson_0.2.21                ellipsis_0.3.2             
  [5] circlize_0.4.13             XVector_0.34.0             
  [7] GlobalOptions_0.1.2         ggdendro_0.1.22            
  [9] clue_0.3-60                 assertive.sets_0.0-3       
 [11] ggrepel_0.9.1               bit64_4.0.5                
 [13] AnnotationDbi_1.56.2        fansi_1.0.2                
 [15] codetools_0.2-18            splines_4.1.2              
 [17] logging_0.10-108            mnormt_2.0.2               
 [19] doParallel_1.0.16           cachem_1.0.6               
 [21] geneplotter_1.72.0          knitr_1.37                 
 [23] Nozzle.R1_1.1-1             broom_0.7.12               
 [25] annotate_1.72.0             cluster_2.1.2              
 [27] png_0.1-7                   readr_2.1.2                
 [29] compiler_4.1.2              httr_1.4.2                 
 [31] backports_1.4.1             Matrix_1.4-0               
 [33] fastmap_1.1.0               limma_3.50.0               
 [35] cli_3.1.1                   lasso2_1.2-22              
 [37] tools_4.1.2                 gtable_0.3.0               
 [39] glue_1.6.1                  GenomeInfoDbData_1.2.7     
 [41] dplyr_1.0.7                 Rcpp_1.0.8                 
 [43] vctrs_0.3.8                 Biostrings_2.62.0          
 [45] nlme_3.1-155                iterators_1.0.13           
 [47] psych_2.1.9                 xfun_0.29                  
 [49] stringr_1.4.0               DEGreport_1.30.0           
 [51] lifecycle_1.0.1             gtools_3.9.2               
 [53] XML_3.99-0.8                edgeR_3.36.0               
 [55] zlibbioc_1.40.0             MASS_7.3-55                
 [57] scales_1.1.1                vroom_1.5.7                
 [59] hms_1.1.1                   parallel_4.1.2             
 [61] RColorBrewer_1.1-2          ComplexHeatmap_2.10.0      
 [63] memoise_2.0.1               gridExtra_2.3              
 [65] ggplot2_3.3.5               reshape_0.8.8              
 [67] stringi_1.7.6               RSQLite_2.2.9              
 [69] genefilter_1.76.0           foreach_1.5.1              
 [71] caTools_1.18.2              BiocParallel_1.28.3        
 [73] shape_1.4.6                 rlang_1.0.0                
 [75] pkgconfig_2.0.3             bitops_1.0-7               
 [77] lattice_0.20-45             purrr_0.3.4                
 [79] cowplot_1.1.1               bit_4.0.4                  
 [81] tidyselect_1.1.1            GGally_2.1.2               
 [83] plyr_1.8.6                  magrittr_2.0.2             
 [85] DESeq2_1.34.0               R6_2.5.1                   
 [87] gplots_3.1.1                generics_0.1.2             
 [89] DelayedArray_0.20.0         DBI_1.1.2                  
 [91] withr_2.4.3                 pillar_1.7.0               
 [93] survival_3.2-13             KEGGREST_1.34.0            
 [95] RCurl_1.98-1.5              tibble_3.1.6               
 [97] crayon_1.4.2                KernSmooth_2.23-20         
 [99] utf8_1.2.2                  tmvnsim_1.0-2              
[101] tzdb_0.2.0                  GetoptLong_1.0.5           
[103] locfit_1.5-9.4              grid_4.1.2                 
[105] blob_1.2.2                  ConsensusClusterPlus_1.58.0
[107] digest_0.6.29               xtable_1.8-4               
[109] tidyr_1.2.0                 munsell_0.5.0

Any Idea for why I am getting this error?

Thank you, Bine

lpantano commented 2 years ago

Hi Bine,

I see the name of the reads don't have the following format: >name_xNN, normally reads in small RNAseq are collapsed into unique sequences and the name is used to mention the counts of each.

There is more information here: https://seqcluster.readthedocs.io/mirna_annotation.html#post-analysis-with-r. The third column on those files need to be the counts for each sequence.

Let me know if you have any other question.

Thanks