compare two sbjs in dev and prod

umccr · Jul 15, 2024 · 6f267d7 · 6f267d7
1 parent 2498f59
commit 6f267d7
Showing 1 changed file with 24 additions and 8 deletions.
diff --git a/inst/scripts/compare_piedb.R b/inst/scripts/compare_piedb.R
@@ -4,19 +4,33 @@ require(here)
 require(glue)
 require(tibble)
 require(tidyr)
+require(DT)
 
-SBJ04426_dev <- readr::read_csv("~/UMCCR/data/wts/RNAsum/reference_update_comp/SBJ04426/dev/genes.expr.perc.csv")
-SBJ04426_pro <- readr::read_csv("~/UMCCR/data/wts/RNAsum/reference_update_comp/SBJ04426/pro/genes.expr.perc.csv")
-SBJ04187_dev <- readr::read_csv("~/UMCCR/data/wts/RNAsum/reference_update_comp/SBJ04187/dev/genes.expr.perc.csv")
-SBJ04187_pro <- readr::read_csv("~/UMCCR/data/wts/RNAsum/reference_update_comp/SBJ04187/pro/genes.expr.perc.csv")
-cancer_genes <- readr::read_tsv("~/UMCCR/research/data/cancer_gene_list/somatic_panel-v24.03.0.tsv")
+SBJ04426_dev <- readr::read_csv("../../data/wts/RNAsum/reference_update_comp/SBJ04426/dev/genes.expr.perc.csv")
+SBJ04426_pro <- readr::read_csv("../../data/wts/RNAsum/reference_update_comp/SBJ04426/pro/genes.expr.perc.csv")
+SBJ04187_dev <- readr::read_csv("../../data/wts/RNAsum/reference_update_comp/SBJ04187/dev/genes.expr.perc.csv")
+SBJ04187_pro <- readr::read_csv("../../data/wts/RNAsum/reference_update_comp/SBJ04187/pro/genes.expr.perc.csv")
+cancer_genes <- readr::read_tsv("../../research/data/cancer_gene_list/somatic_panel-v24.03.0.tsv")
 
 # now explore expression differences in reference and patient columns
 # between dev and prod.
 SBJ04426_df <- dplyr::left_join(SBJ04426_dev, SBJ04426_pro, by = "Gene", suffix = c(".dev", ".pro")) |>
   dplyr::mutate(
-    # Ref_equal = `KIRP (TCGA).dev` == `KIRP (TCGA).pro`,
-    # Ref_equal = `PANCAN (TCGA).dev` == `PANCAN (TCGA).pro`,
+    Ref_equal = `BRCA (TCGA).dev` == `BRCA (TCGA).pro`,
+    Pat_equal = Patient.dev == Patient.pro,
+    # Ref_diff = abs(`PANCAN (TCGA).dev` - `PANCAN (TCGA).pro`),
+    Ref_diff = abs(`BRCA (TCGA).dev` - `BRCA (TCGA).pro`),
+    Pat_diff = abs(Patient.dev - Patient.pro)
+  ) |>
+  dplyr::select(Gene, contains("BRCA"), contains("PANCAN"), Ref_diff, contains("Patient"), Pat_diff, contains("equal")) |>
+  dplyr::filter(Pat_diff > 0) |>
+  dplyr::filter(Gene %in% cancer_genes$ensembl_gene_symbol) |>
+  dplyr::arrange(desc(Pat_diff)) |>
+  dplyr::arrange(desc(Ref_diff)) |>
+  datatable()
+
+SBJ04187_df <- dplyr::left_join(SBJ04187_dev, SBJ04187_pro, by = "Gene", suffix = c(".dev", ".pro")) |>
+  dplyr::mutate(
     Ref_equal = `BRCA (TCGA).dev` == `BRCA (TCGA).pro`,
     Pat_equal = Patient.dev == Patient.pro,
     # Ref_diff = abs(`PANCAN (TCGA).dev` - `PANCAN (TCGA).pro`),
@@ -31,4 +45,6 @@ SBJ04426_df <- dplyr::left_join(SBJ04426_dev, SBJ04426_pro, by = "Gene", suffix
   datatable()
 
 # plot Ref_diff values
-hist(SBJ04426_df$Ref_diff, breaks = 100)
+hist(SBJ04426_df[[1]]$data$Ref_diff, breaks = 100)
+
+