tximeta Error in UseMethod("filter_")
1
1
Entering edit mode
@pufall-miles-a-5909
Last seen 23 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:

meta_sep 
# 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 -

Miles

sessionInfo()
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

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] 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] 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 • 98 views
ADD COMMENT
1
Entering edit mode
@mikelove
Last seen 4 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.

ADD COMMENT

Login before adding your answer.

Traffic: 544 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6