EpiCompare report replacing Get started vignette

[bschilder]

Issue

The "Get started" vignette it getting replaced by the EpiCompare report generated in the example, which also happens to be an html file of the same name. This means the wrong file is getting displayed on the website.

https://neurogenomics.github.io/EpiCompare/articles/EpiCompare.html

Solution

Change the output directory or name of the EpiCompare report in the vignette.

[bschilder]

Oddly, the file should already be written to the temp directory. Not sure why it's getting placed in the vignette folder instead. Maybe it's coming from elsewhere (one of the examples?)

EpiCompare(peakfiles = peaklist,
           genome_build = "hg19",
           blacklist = hg19_blacklist,
           picard_files = picard,
           reference = reference_peak,
           upset_plot = FALSE,
           stat_plot = FALSE,
           chromHMM_plot = FALSE,
           chromHMM_annotation = "K562",
           chipseeker_plot = FALSE,
           enrichment_plot = FALSE,
           tss_plot = FALSE,
           interact = FALSE,
           save_output = FALSE,
           output_filename = "EpiCompare",
           output_timestamp = FALSE,
           output_dir = tempdir())

Tried changing this arg:

           output_filename = "EpiCompare_test",