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pachterlab / sleuth

Differential analysis of RNA-Seq
http://pachterlab.github.io/sleuth
GNU General Public License v3.0
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Error in UseMethod("filter_") #255

Closed helmutcarter closed 3 years ago

helmutcarter commented 3 years ago

I am following the guide at https://pachterlab.github.io/sleuth_walkthroughs/trapnell/analysis.html using my own data. When I run the following command in RStudio: t2g <- biomaRt::getBM(attributes = c("ensembl_transcript_id", "ensembl_gene_id", "external_gene_name"), mart = mart)

I get the error: 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')"

My sessionInfo() looks like this:

R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] biomaRt_2.42.1       sleuth_0.30.0        maser_1.4.0          GenomicRanges_1.38.0 GenomeInfoDb_1.22.1  IRanges_2.20.2       S4Vectors_0.24.4    
[8] BiocGenerics_0.32.0  ggplot2_3.3.3

Thanks!

helmutcarter commented 3 years ago

Updating to the latest version of R fixed it. Thanks