Merge pull request #55 from mskilab/as.dev

save purity ploidy values to a table
mskilab-org · Nov 25, 2021 · 5db9153 · 5db9153
2 parents 8d97476 + 430011b
commit 5db9153
Showing 1 changed file with 5 additions and 0 deletions.
diff --git a/R/JaBbA.R b/R/JaBbA.R
@@ -718,6 +718,7 @@ jabba_stub = function(junctions, # path to junction VCF file, dRanger txt file o
     jabba.simple.gg.rds.file = paste(outdir, 'jabba.simple.gg.rds', sep = '/')
     jabba.simple.vcf.file = paste(outdir, 'jabba.simple.vcf', sep = '/')
     jabba.simple.cnv.vcf.file = paste(outdir, 'jabba.simple.cnv.vcf', sep = '/')
+    purity.ploidy.txt.file = paste(outdir, 'purity.ploidy.txt', sep = '/')
     jabba.png.file = paste(outdir, 'jabba.png', sep = '/')
     jabba.simple.png.file = paste(outdir, 'jabba.simple.png', sep = '/')
     seg.tab.file = paste(outdir, 'jabba.seg', sep = '/')
@@ -1427,6 +1428,10 @@ jabba_stub = function(junctions, # path to junction VCF file, dRanger txt file o
         saveRDS(jabd, jabba.rds.file)
         saveRDS(jabd.simple, jabba.simple.rds.file)
 
+        purity.ploidy.dt = data.table(purity = jab$purity,
+                                      ploidy = jab$ploidy)
+        fwrite(purity.ploidy.dt, purity.ploidy.txt.file, sep = '\t')
+
         jab.gg = gGnome::gGraph$new(jab = jabd)
         tmp.jabd.simple = jabd.simple
         values(tmp.jabd.simple$junctions)$cn = NULL