compare expression values between full vs partial tcga cohort

inst/scripts/compare_piedb.R

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+require(dplyr)
+require(readr)
+require(here)
+require(glue)
+require(tibble)
+require(tidyr)
+
+dev <- readr::read_csv("~/UMCCR/data/wts/RNAsum/reference_update_comp/SBJ04426/dev/genes.expr.perc.csv")
+pro <- readr::read_csv("~/UMCCR/data/wts/RNAsum/reference_update_comp/SBJ04426/pro/genes.expr.perc.csv")
+dev <- readr::read_csv("~/UMCCR/data/wts/RNAsum/reference_update_comp/SBJ04187/dev/genes.expr.perc.csv")
+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")
+
+# now explore expression differences in reference and patient columns
+# between dev and prod.
+df <- dplyr::left_join(dev, 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$ensembl_gene_symbol) |>
+  dplyr::arrange(desc(Pat_diff)) |>
+  dplyr::arrange(desc(Ref_diff)) |>
+  datatable()
+
+# plot Ref_diff values
+hist(df$Ref_diff, breaks = 100)