bug fix

taylor-lab · Feb 10, 2020 · 1f5b1c5 · 1f5b1c5
1 parent 57a8a1b
commit 1f5b1c5
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: facetsSuite
 Type: Package
 Title: Functions to run and parse output from FACETS
-Version: 2.0.0
+Version: 2.0.2
 Authors@R: person(given = "Philip",
              family = "Jonsson",
              role = c("aut", "cre"),

diff --git a/R/ccf-annotate-maf.R b/R/ccf-annotate-maf.R
@@ -61,10 +61,10 @@ ccf_annotate_maf = function(maf,
     maf[, c('ccf_Mcopies', 'ccf_Mcopies_lower', 'ccf_Mcopies_upper', 'ccf_Mcopies_prob95', 'ccf_Mcopies_prob90') :=
             estimate_ccf(purity, tcn, tcn - lcn, t_alt_count, t_depth), by = seq_len(nrow(maf))]
     maf[, c('ccf_1copy', 'ccf_1copy_lower', 'ccf_1copy_upper', 'ccf_1copy_prob95', 'ccf_1copy_prob90') :=
-            estimate_ccf(purity, tcn, tcn - lcn, t_alt_count, t_depth), by = seq_len(nrow(maf))]
+            estimate_ccf(purity, tcn, 1, t_alt_count, t_depth), by = seq_len(nrow(maf))]
     maf[, c('ccf_expected_copies', 'ccf_expected_copies_lower', 'ccf_expected_copies_upper',
             'ccf_expected_copies_prob95', 'ccf_expected_copies_prob90') :=
-            estimate_ccf(purity, tcn, tcn - lcn, t_alt_count, t_depth), by = seq_len(nrow(maf))]
+            estimate_ccf(purity, tcn, expected_alt_copies, t_alt_count, t_depth), by = seq_len(nrow(maf))]
     as.data.frame(maf)
 }