Entering edit mode
I am working through the Analyzing RNA-seq data with DESeq2 tutorial, and running it through RMarkdown.
Loading the tximeta package in the tutorial code below:
coldata <- samples
coldata$files <- files
coldata$names <- coldata$run
library("tximeta")
# se <- tximeta(coldata)
# ddsTxi <- DESeqDataSet(se, design = ~ condition)
Is causing the following error message:
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')"
From the win-library DESCRIPTION file the version of tximeta is:
Package: tximeta Version: 1.2.2
Suggestions for how to get past this would be greatly appreciated.
sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows >= 8 (build 9200)
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] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.6.0 fastmap_1.1.0 htmltools_0.5.2 tools_3.6.0 yaml_2.2.1 rmarkdown_2.11
[7] knitr_1.36 xfun_0.28 digest_0.6.29 rlang_0.4.12 evaluate_0.14