neurogenomics / EpiCompare

Comparison, benchmarking & QC of epigenetic datasets
https://doi.org/doi:10.18129/B9.bioc.EpiCompare
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Supply message indicating which feature were NOT run #145

Closed bschilder closed 1 year ago

bschilder commented 1 year ago

EpiCompare::EpiCompare() has a lot of arguments, most of which are set to FALSE by default to speed up examples and let users get up and running with a minimal version right away (which is helpful when trying to figure out whether errors are due to your data or how the pipeline is configured).

However, we'd still like to make users aware of all the features EpiCompare has to offer, even if they don't read the documentation. So I'll add a message letting users know which features they are NOT using currently.

bschilder commented 1 year ago

Now implemented as new internal function, called within EpiCompare::EpiCompare:

check_unused_args(upset_plot=upset_plot, 
                    stat_plot=stat_plot, 
                    chromHMM_plot=chromHMM_plot, 
                    chipseeker_plot=chipseeker_plot, 
                    enrichment_plot=enrichment_plot, 
                    tss_plot=tss_plot, 
                    precision_recall_plot=precision_recall_plot, 
                    corr_plot=corr_plot)  
NOTE: The following EpiCompare features are NOT being used: 
 - upset_plot=
 - stat_plot=
 - chromHMM_plot=
 - chipseeker_plot=
 - enrichment_plot=
 - tss_plot=
 - precision_recall_plot=
 - corr_plot=