Error in UseMethod("filter_") for RIPSeeker package
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Yongqing • 0
@yongqing-24956
Last seen 6 months ago

Enter the body of text here

Code should be placed in three backticks as shown below

library(RIPSeeker)

# Retrieve system files
  extdata.dir <- system.file("extdata", package="RIPSeeker") 

  bamFiles <- list.files(extdata.dir, ".bam$", recursive=TRUE, full.names=TRUE)

  bamFiles <- grep("PRC2", bamFiles, value=TRUE)

  cNAME <- "SRR039214"                      # specify control name

  # output file directory
  outDir <- paste(getwd(), "ripSeek_example", sep="/")

  # Parameters setting
  binSize <- NULL                           # automatically determine bin size
  minBinSize <- 10000                       # min bin size in automatic bin size selection
  maxBinSize <- 12000                       # max bin size in automatic bin size selection
  multicore <- TRUE                     # use multicore
  strandType <- "-"                     # set strand type to minus strand

  biomart <- "ENSEMBL_MART_ENSEMBL"     # use archive to get ensembl 65
  dataset <- "mmusculus_gene_ensembl"       # mouse dataset id name 
  host <- "may2012.archive.ensembl.org"     # use ensembl 65 for annotation

  goAnno <- "org.Mm.eg.db"

  ################ run main function ripSeek to predict RIP ################
  seekOut <- ripSeek(bamPath=bamFiles, cNAME=cNAME, 
                     binSize=binSize, minBinSize = minBinSize, 
                     maxBinSize = maxBinSize, strandType=strandType, 
                     outDir=outDir, silentMain=FALSE,
                     verbose=TRUE, reverseComplement=TRUE, genomeBuild="mm9",
                     biomart=biomart, host=host,
                     biomaRt_dataset = dataset,
                     goAnno = goAnno,
                     uniqueHit = TRUE, assignMultihits = TRUE, 
                     rerunWithDisambiguatedMultihits = TRUE, multicore=multicore)



# include your problematic code here with any corresponding output 


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')"


# please also include the results of running the following in an R session 

sessionInfo( )

R version 3.6.3 (2020-02-29) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages: [1] ChIPpeakAnno_3.20.1 VennDiagram_1.6.20 futile.logger_1.4.3
[4] biomaRt_2.42.1 memoise_2.0.0 RIPSeeker_1.26.0
[7] rtracklayer_1.46.0 GenomicAlignments_1.22.1 Rsamtools_2.2.3
[10] Biostrings_2.54.0 XVector_0.26.0 SummarizedExperiment_1.16.1 [13] DelayedArray_0.12.3 BiocParallel_1.20.1 matrixStats_0.58.0
[16] Biobase_2.46.0 GenomicRanges_1.38.0 GenomeInfoDb_1.22.1
[19] IRanges_2.20.2 S4Vectors_0.24.4 BiocGenerics_0.32.0

loaded via a namespace (and not attached): [1] ProtGenerics_1.18.0 bitops_1.0-6 bit64_4.0.5 progress_1.2.2
[5] httr_1.4.2 tools_3.6.3 utf8_1.1.4 R6_2.5.0
[9] DBI_1.1.1 lazyeval_0.2.2 ade4_1.7-16 tidyselect_1.1.0
[13] prettyunits_1.1.1 bit_4.0.4 curl_4.3 compiler_3.6.3
[17] graph_1.64.0 formatR_1.7 RBGL_1.62.1 askpass_1.1
[21] rappdirs_0.3.3 stringr_1.4.0 pkgconfig_2.0.3 dbplyr_2.1.0
[25] fastmap_1.1.0 ensembldb_2.10.2 limma_3.42.2 BSgenome_1.54.0
[29] regioneR_1.18.1 rlang_0.4.10 rstudioapi_0.13 RSQLite_2.2.3
[33] generics_0.1.0 dplyr_1.0.4 RCurl_1.98-1.2 magrittr_2.0.1
[37] GO.db_3.10.0 GenomeInfoDbData_1.2.2 Matrix_1.2-18 Rcpp_1.0.6
[41] fansi_0.4.2 lifecycle_1.0.0 stringi_1.5.3 MASS_7.3-51.5
[45] zlibbioc_1.32.0 BiocFileCache_1.10.2 blob_1.2.1 crayon_1.4.1
[49] lattice_0.20-38 splines_3.6.3 multtest_2.42.0 GenomicFeatures_1.38.2 [53] hms_1.0.0 pillar_1.5.0 seqinr_4.2-5 futile.options_1.0.1
[57] XML_3.99-0.3 glue_1.4.2 lambda.r_1.2.4 BiocManager_1.30.10
[61] idr_1.2 vctrs_0.3.6 openssl_1.4.3 purrr_0.3.4
[65] assertthat_0.2.1 cachem_1.0.4 AnnotationFilter_1.10.0 survival_3.1-8
[69] tibble_3.1.0 AnnotationDbi_1.48.0 ellipsis_0.3.1

biomaRt Bioconductor-RIPSeeker • 236 views
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Entering edit mode
Mike Smith ★ 5.1k
@mike-smith
Last seen 48 minutes ago
EMBL Heidelberg / de.NBI

This is actually the result of a change in the dplyr package. You're using fairly old versions of R and Bioconductor, and so the copies of the packages that you have installed are not compatible with this new dplyr. There's quite a few posts on here about the issue e.g. Answer: BiomaRt::getBM Error in UseMethod(filter_)

Two possible solutions are to either upgrade R and Bioconductor to the latest release versions, or downgrade dplyr (and make sure R doesn't automatically update it every time you install something else).

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