Updated deep loss CNV calls

analyses/focal-cn-file-preparation/04-prepare-cn-file.R

@@ -240,9 +240,10 @@ cnv_no_xy <- cnv_df %>%
 # Merge and annotated no X&Y
 autosome_annotated_cn <- process_annotate_overlaps(cnv_df = cnv_no_xy,
                                                    txdb_exons = tx_exons) %>%
-  # mark possible amplifications in autosomes
+  # mark possible amplifications and deep loss in autosomes
   dplyr::mutate(status = dplyr::case_when(
     copy_number > (2 * ploidy) ~ "amplification",
+    copy_number == 0 ~ "deep deletion",
     TRUE ~ status
   ))
 
@@ -264,7 +265,13 @@ if (xy_flag) {
 
   # Merge and annotated no X&Y
   sex_chrom_annotated_cn <- process_annotate_overlaps(cnv_df = cnv_sex_chrom,
-                                                      txdb_exons = tx_exons)
+                                                      txdb_exons = tx_exons) %>%
+  # mark possible deep loss in sex chromosome
+  dplyr::mutate(status = dplyr::case_when(
+    copy_number == 0  ~ "deep deletion",
+    TRUE ~ status
+  )) 
+
 
   # Add germline sex estimate into this data.frame
   sex_chrom_annotated_cn <- sex_chrom_annotated_cn %>%

analyses/focal-cn-file-preparation/README.md

@@ -46,6 +46,7 @@ See the notebook for more information. This notebook also prepares lists of copy
   | biospecimen_id | status | copy_number | ploidy | ensembl | gene_symbol | cytoband |
   |----------------|--------|-------------|--------|---------|-------------|---------|
   Any segment that is copy neutral is filtered out of this table. In addition, [any segments with copy number > (2 * ploidy) are marked as amplifications](https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/e2058dd43d9b1dd41b609e0c3429c72f79ff3be6/analyses/focal-cn-file-preparation/03-prepare-cn-file.R#L275) in the `status` column.
+  Any segment that is copy neutral is filtered out of this table. In addition, [any segments with copy number <= (ploidy -2 ) in autosomes chromosomes](https://github.com/kgaonkar6/OpenPBTA-analysis/blob/5e9b68ed0c37d6c87bc67ee1f95be9e47ec9b4ca/analyses/focal-cn-file-preparation/04-prepare-cn-file.R#L244-L247) and [copy_number==0 in X/Y chromosomes are marked as deep deletions](https://github.com/kgaonkar6/OpenPBTA-analysis/blob/5e9b68ed0c37d6c87bc67ee1f95be9e47ec9b4ca/analyses/focal-cn-file-preparation/04-prepare-cn-file.R#L270-L272) in the `status` column.
 
 * `05-define-most-focal-cn-units.Rmd` - This notebook defines the _most focal_ recurrent copy number units by removing focal changes that are within entire chromosome arm losses and gains.
 _Most focal_ here meaning if a chromosome arm is not clearly defined as a gain or loss (and is callable) we look to define the cytoband level status.