tximeta Error in UseMethod("filter_")
Entering edit mode
Last seen 26 days ago
United States

I have 10 data sets that I've mapped to the Gencode transcriptome using salmon. I made a coldata table that shows where they are:

# A tibble: 10 x 3
   names      background files                                      
   <chr>      <chr>      <chr>                                      
 1 SRR4000492 FCRL5-     ~/hpchome/b_cell/quants/SRR4000492/quant.sf
 2 SRR4000493 FCRL5-     ~/hpchome/b_cell/quants/SRR4000493/quant.sf
 3 SRR4000494 FCRL5-     ~/hpchome/b_cell/quants/SRR4000494/quant.sf
 4 SRR4000495 FCRL5-     ~/hpchome/b_cell/quants/SRR4000495/quant.sf
 5 SRR4000496 FCRL5-     ~/hpchome/b_cell/quants/SRR4000496/quant.sf
 6 SRR4000497 FCRL5+     ~/hpchome/b_cell/quants/SRR4000497/quant.sf
 7 SRR4000498 FCRL5+     ~/hpchome/b_cell/quants/SRR4000498/quant.sf
 8 SRR4000499 FCRL5+     ~/hpchome/b_cell/quants/SRR4000499/quant.sf
 9 SRR4000500 FCRL5+     ~/hpchome/b_cell/quants/SRR4000500/quant.sf
10 SRR4000501 FCRL5+     ~/hpchome/b_cell/quants/SRR4000501/quant.sf

I tried to import the count tables using tximeta and got the following error:

se <- tximeta(meta_sep)
importing quantifications
reading in files with read_tsv
1 2 3 4 5 6 7 8 9 10 
Error in UseMethod("filter_") : 
  no applicable method for 'filter_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"

I poked around on-line and found that this could be because I am using an old version of R (3.6.1) and Bioconductor (3.10) where there may be a conflict between dplyr and biomaRt. Both R and Bioconductor are installed on a cluster, are used for class, and are nto easily upgraded. Is there another solution to this issue?

Thanks -


R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Matrix products: default
BLAS:   /opt/R/lib/R/lib/libRblas.so
LAPACK: /opt/R/lib/R/lib/libRlapack.so

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              

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

other attached packages:
 [1] TxDb.Mmusculus.UCSC.mm10.knownGene_3.10.0 rjson_0.2.20                             
 [3] ggpubr_0.4.0                              qvalue_2.18.0                            
 [5] viridis_0.6.0                             viridisLite_0.4.0                        
 [7] ReportingTools_2.26.0                     knitr_1.32                               
 [9] genefilter_1.68.0                         apeglm_1.8.0                             
[11] PoiClaClu_1.0.2.1                         RColorBrewer_1.1-2                       
[13] pheatmap_1.0.12                           hexbin_1.28.2                            
[15] vsn_3.54.0                                ensembldb_2.10.2                         
[17] AnnotationFilter_1.10.0                   GenomicFeatures_1.38.2                   
[19] AnnotationDbi_1.48.0                      rhdf5_2.30.1                             
[21] DESeq2_1.26.0                             SummarizedExperiment_1.16.1              
[23] DelayedArray_0.12.3                       BiocParallel_1.20.1                      
[25] matrixStats_0.58.0                        Biobase_2.46.0                           
[27] GenomicRanges_1.38.0                      GenomeInfoDb_1.22.1                      
[29] IRanges_2.20.2                            S4Vectors_0.24.4                         
[31] BiocGenerics_0.32.0                       tximeta_1.4.5                            
[33] tximportData_1.14.0                       tximport_1.14.2                          
[35] forcats_0.5.1                             stringr_1.4.0                            
[37] dplyr_1.0.4                               purrr_0.3.4                              
[39] readr_1.4.0                               tidyr_1.1.3                              
[41] tibble_3.1.0                              ggplot2_3.3.3                            
[43] tidyverse_1.3.1                          

loaded via a namespace (and not attached):
  [1] utf8_1.2.1               R.utils_2.10.1           tidyselect_1.1.0         RSQLite_2.2.6           
  [5] htmlwidgets_1.5.3        grid_3.6.1               munsell_0.5.0            preprocessCore_1.48.0   
  [9] withr_2.4.1              colorspace_2.0-0         Category_2.52.1          OrganismDbi_1.28.0      
 [13] rstudioapi_0.13          ggsignif_0.6.1           labeling_0.4.2           bbmle_1.0.23.1          
 [17] GenomeInfoDbData_1.2.2   hwriter_1.3.2            farver_2.1.0             bit64_4.0.5             
 [21] coda_0.19-4              vctrs_0.3.7              generics_0.1.0           xfun_0.22               
 [25] biovizBase_1.34.1        BiocFileCache_1.10.2     R6_2.5.0                 locfit_1.5-9.4          
 [29] bitops_1.0-6             cachem_1.0.4             reshape_0.8.8            assertthat_0.2.1        
 [33] scales_1.1.1             nnet_7.3-15              gtable_0.3.0             affy_1.64.0             
 [37] ggbio_1.34.0             rlang_0.4.10             splines_3.6.1            rstatix_0.7.0           
 [41] rtracklayer_1.46.0       lazyeval_0.2.2           dichromat_2.0-0          broom_0.7.6             
 [45] checkmate_2.0.0          abind_1.4-5              BiocManager_1.30.12      yaml_2.2.1              
 [49] reshape2_1.4.4           modelr_0.1.8             backports_1.2.1          Hmisc_4.5-0             
 [53] RBGL_1.62.1              tools_3.6.1              affyio_1.56.0            ellipsis_0.3.1          
 [57] Rcpp_1.0.6               plyr_1.8.6               base64enc_0.1-3          progress_1.2.2          
 [61] zlibbioc_1.32.0          RCurl_1.98-1.3           prettyunits_1.1.1        rpart_4.1-15            
 [65] openssl_1.4.3            haven_2.4.0              cluster_2.1.2            fs_1.5.0                
 [69] magrittr_2.0.1           data.table_1.14.0        openxlsx_4.2.3           reprex_2.0.0            
 [73] mvtnorm_1.1-1            ProtGenerics_1.18.0      evaluate_0.14            hms_1.0.0               
 [77] xtable_1.8-4             XML_3.99-0.3             rio_0.5.26               emdbook_1.3.12          
 [81] jpeg_0.1-8.1             readxl_1.3.1             gridExtra_2.3            compiler_3.6.1          
 [85] biomaRt_2.42.1           bdsmatrix_1.3-4          crayon_1.4.1             R.oo_1.24.0             
 [89] htmltools_0.5.1.1        GOstats_2.52.0           mgcv_1.8-34              Formula_1.2-4           
 [93] geneplotter_1.64.0       lubridate_1.7.10         DBI_1.1.1                dbplyr_2.1.1            
 [97] MASS_7.3-53.1            rappdirs_0.3.3           car_3.0-10               Matrix_1.3-2            
[101] cli_2.4.0                R.methodsS3_1.8.1        pkgconfig_2.0.3          GenomicAlignments_1.22.1
[105] numDeriv_2016.8-1.1      foreign_0.8-71           xml2_1.3.2               annotate_1.64.0         
[109] XVector_0.26.0           AnnotationForge_1.28.0   rvest_1.0.0              VariantAnnotation_1.32.0
[113] digest_0.6.27            graph_1.64.0             Biostrings_2.54.0        rmarkdown_2.7           
[117] cellranger_1.1.0         htmlTable_2.1.0          edgeR_3.28.1             GSEABase_1.48.0         
[121] curl_4.3                 Rsamtools_2.2.3          nlme_3.1-152             lifecycle_1.0.0         
[125] jsonlite_1.7.2           PFAM.db_3.10.0           Rhdf5lib_1.8.0           carData_3.0-4           
[129] askpass_1.1              limma_3.42.2             BSgenome_1.54.0          fansi_0.4.2             
[133] pillar_1.6.0             lattice_0.20-41          GGally_2.1.1             fastmap_1.1.0           
[137] httr_1.4.2               survival_3.2-10          GO.db_3.10.0             glue_1.4.2              
[141] zip_2.1.1                png_0.1-7                bit_4.0.4                Rgraphviz_2.30.0        
[145] stringi_1.5.3            blob_1.2.1               latticeExtra_0.6-29      memoise_2.0.0  sessionInfo( )
tximeta • 103 views
Entering edit mode
Last seen 7 hours ago
United States

Could you try as.data.frame(coldata) before providing to tximeta? I may need to have a more explicit argument check there, as there could be some method conflicts on the tibble.


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