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Excel output not generated when simplify_ontologies = FALSE #2

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paulklemm opened this issue Jan 10, 2020 · 2 comments
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Excel output not generated when simplify_ontologies = FALSE #2

paulklemm opened this issue Jan 10, 2020 · 2 comments
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@paulklemm
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Bug: Excel output not generated when simplify_ontologies = FALSE

@paulklemm paulklemm self-assigned this Jan 10, 2020
@paulklemm
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This is not the case, the Excel table is generally not put out at the moment

@paulklemm
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For some weird reason, the RMarkdown passed parameters were not honored. My previous debug method fixed this issue without me knowing it I'm having one.

I now resorted to having the following solution. In the beginning of my setup chunk, I'll pass all parameters to a custom list.

rmd_params <- list()
rmd_params$dat <- params$dat
rmd_params$output_path <- params$output_path
rmd_params$save_excel <- params$save_excel
rmd_params$significance_cutoff <- params$significance_cutoff
rmd_params$simplify_ontologies <- params$simplify_ontologies
rmd_params$do_gse <- params$do_gse
rmd_params$use_background <- params$use_background

From that point on, I will only use this list to access parameters.

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