[Bioc-devel] Reference inst/extdata files in vignette

alan murphy @|@nmurph94 @end|ng |rom hotm@||@com
Thu Apr 22 12:54:40 CEST 2021

Hi all,

I'm working on the development of MungeSumstats(https://github.com/neurogenomics/MungeSumstats) and am trying to reference raw data files (txt and VCF) in my vignette. These files are stored in `inst/extdata` but when I try load then with the below it fails on Bioconductor checks but will pass local checks:

eduAttainOkbayPth <- system.file("extdata","eduAttainOkbay.txt", package="MungeSumstats")

reformatted <-   MungeSumstats::format_sumstats(path=eduAttainOkbayPth,ref_genome="GRCh37")
The error is caused by a validation check I have to ensure the path passed to `format_sumstats` is valid. Locally this works (see below) but I get an error on Bioconductor:

> file.exists(eduAttainOkbayPth)[1]

Does anyone know of the correct way to access raw data files like text files?

Kind regards,

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