AlexsLemonade · kgaonkar6 · Apr 2, 2021 · Apr 6, 2021 · Apr 6, 2021 · Apr 7, 2021
diff --git a/analyses/copy_number_consensus_call/--configfile b/analyses/copy_number_consensus_call/--configfile
diff --git a/analyses/copy_number_consensus_call/--restart-times b/analyses/copy_number_consensus_call/--restart-times
diff --git a/analyses/copy_number_consensus_call/-j b/analyses/copy_number_consensus_call/-j
diff --git a/analyses/copy_number_consensus_call/-s b/analyses/copy_number_consensus_call/-s
diff --git a/analyses/copy_number_consensus_call/results/pbta-cnv-consensus.seg.gz b/analyses/copy_number_consensus_call/results/pbta-cnv-consensus.seg.gz
diff --git a/analyses/copy_number_consensus_call/run_consensus_call.sh b/analyses/copy_number_consensus_call/run_consensus_call.sh
diff --git a/analyses/copy_number_consensus_call/scripts/bed_to_segfile.R b/analyses/copy_number_consensus_call/scripts/bed_to_segfile.R
@@ -123,8 +123,8 @@ cnvs <- cnvs %>%
                 segmean = purrr::map_dbl(cnvkit_df, segmean_function),
                 cnvkit_cn = purrr::map_dbl(cnvkit_df, copies_wmedian),
                 freec_cn = purrr::map_dbl(freec_df, copies_wmedian),
-                copynum = ifelse(is.finite(cnvkit_cn), # use cnvkit if available
-                                 cnvkit_cn, freec_cn), #otherwise use freec
+                copynum = ifelse(is.finite(freec_cn), # use freec if available
+                                 freec_cn, cnvkit_cn), #otherwise use cnvkit
                 num.mark = NA)
 
 

diff --git a/analyses/focal-cn-file-preparation/02-add-ploidy-consensus.nb.html b/analyses/focal-cn-file-preparation/02-add-ploidy-consensus.nb.html
diff --git a/analyses/focal-cn-file-preparation/03-add-cytoband-status-consensus.nb.html b/analyses/focal-cn-file-preparation/03-add-cytoband-status-consensus.nb.html
diff --git a/analyses/focal-cn-file-preparation/05-define-most-focal-cn-units.nb.html b/analyses/focal-cn-file-preparation/05-define-most-focal-cn-units.nb.html
diff --git a/analyses/focal-cn-file-preparation/06-find-recurrent-calls.nb.html b/analyses/focal-cn-file-preparation/06-find-recurrent-calls.nb.html
diff --git a/analyses/focal-cn-file-preparation/plots/all_histology_cn_counts.png b/analyses/focal-cn-file-preparation/plots/all_histology_cn_counts.png
diff --git a/...-preparation/plots/consensus_seg_annotated_cn_autosomes_polya_loss_cor_plot.png b/...-preparation/plots/consensus_seg_annotated_cn_autosomes_polya_loss_cor_plot.png
diff --git a/...e-preparation/plots/consensus_seg_annotated_cn_autosomes_polya_stacked_plot.png b/...e-preparation/plots/consensus_seg_annotated_cn_autosomes_polya_stacked_plot.png
diff --git a/...-preparation/plots/consensus_seg_annotated_cn_autosomes_polya_zero_cor_plot.png b/...-preparation/plots/consensus_seg_annotated_cn_autosomes_polya_zero_cor_plot.png
diff --git a/...reparation/plots/consensus_seg_annotated_cn_autosomes_stranded_stacked_plot.png b/...reparation/plots/consensus_seg_annotated_cn_autosomes_stranded_stacked_plot.png
diff --git a/...le-preparation/plots/consensus_seg_annotated_cn_x_and_y_polya_loss_cor_plot.png b/...le-preparation/plots/consensus_seg_annotated_cn_x_and_y_polya_loss_cor_plot.png
diff --git a/...ile-preparation/plots/consensus_seg_annotated_cn_x_and_y_polya_stacked_plot.png b/...ile-preparation/plots/consensus_seg_annotated_cn_x_and_y_polya_stacked_plot.png
diff --git a/...le-preparation/plots/consensus_seg_annotated_cn_x_and_y_polya_zero_cor_plot.png b/...le-preparation/plots/consensus_seg_annotated_cn_x_and_y_polya_zero_cor_plot.png
diff --git a/...-preparation/plots/consensus_seg_annotated_cn_x_and_y_stranded_stacked_plot.png b/...-preparation/plots/consensus_seg_annotated_cn_x_and_y_stranded_stacked_plot.png
diff --git a/analyses/focal-cn-file-preparation/plots/separate_histology_cn_counts.png b/analyses/focal-cn-file-preparation/plots/separate_histology_cn_counts.png
diff --git a/analyses/focal-cn-file-preparation/results/consensus_seg_annotated_cn_autosomes.tsv.gz b/analyses/focal-cn-file-preparation/results/consensus_seg_annotated_cn_autosomes.tsv.gz
diff --git a/analyses/focal-cn-file-preparation/results/consensus_seg_annotated_cn_x_and_y.tsv.gz b/analyses/focal-cn-file-preparation/results/consensus_seg_annotated_cn_x_and_y.tsv.gz
diff --git a/analyses/focal-cn-file-preparation/results/consensus_seg_focal_cn_recurrent_genes.tsv b/analyses/focal-cn-file-preparation/results/consensus_seg_focal_cn_recurrent_genes.tsv
@@ -1,23 +1,23 @@
 gene
+FAM122A
+LINC01506
+PGM5
+PIP5K1B
+TMEM252
+TMEM252-DT
+UBE2L3
 BANCR
 C22orf39
 CDC45
 CLDN5
-FAM122A
 FXN
 GNB1L
 HIRA
-LINC01506
 MIR130B
 MIR301B
-PGM5
 PIEZO2
-PIP5K1B
 PPIL2
 PRKACG
 TJP2
-TMEM252
-TMEM252-DT
-UBE2L3
 UFD1
 YPEL1
diff --git a/analyses/focal-cn-file-preparation/results/consensus_seg_most_focal_cn_status.tsv.gz b/analyses/focal-cn-file-preparation/results/consensus_seg_most_focal_cn_status.tsv.gz