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MaxLChao / gGnome

R API for browsing, analyzing, and manipulating reference-aligned genome graphs in a GenomicRanges framework
http://mskilab.com/gGnome/tutorial.html
MIT License
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pgv fails if we pass an already created PGV dir #1

Open MaxLChao opened 1 year ago

MaxLChao commented 1 year ago 
> pgvtest = gGnome::pgv(sup_enh_dt, dataset_name = "superenhancers_DavisTNBC",
+                       name.col = "pair", outdir = "~/public_html/PGV/",
+                       cov.col = 'tumor_dryclean_cov', gg.col = 'superenh_prox',
+                       cov.field = 'foreground', ref = 'hg19',
+                       cov.bin.width = '1e4', overwrite = F, append = T, 
+                       cid.field = NULL, connections.associations = F,
+                       mc.cores = 10)

passing a dir that was created externally (i.e. mkdir ~/public_html/PGV)

will create an error:

Error in is.dir.a.PGV.instance(outdir) : 
  /gpfs/commons/projects/imielinski_web/mchao/PGV does not seem to be a proper clone of the PGV github repository.