pcgr: handle tmb v_stat (fixes #99)

umccr · Sep 29, 2023 · c3aa59f · c3aa59f
1 parent 8213fc2
commit c3aa59f
Showing 1 changed file with 7 additions and 5 deletions.
diff --git a/R/pcgr.R b/R/pcgr.R
@@ -32,17 +32,19 @@ PcgrJsonFile <- R6::R6Class(
       #   purrr::map(l2tib) |>
       #   dplyr::bind_rows(.id = "name_tidy") |>
       #   dplyr::select("name", "name_tidy", "version", "url", "resource_type")
-      tmb <- j[["content"]][["tmb"]][["variant_statistic"]]
-      # handle nulls
-      tmb <- tmb %||% list(tmb_estimate = NA, n_tmb = NA)
+      # handle nulls and rename - see umccr/dracarys#99
+      tmb <-
+        j[["content"]][["tmb"]][["variant_statistic"]] %||%
+        j[["content"]][["tmb"]][["v_stat"]] %||%
+        list(tmb_estimate = NA, n_tmb = NA)
       tmb <- purrr::flatten(tmb) |>
-        tibble::as_tibble() |>
+        tibble::as_tibble_row() |>
         dplyr::select("tmb_estimate", "n_tmb")
       msi <- j[["content"]][["msi"]][["prediction"]][["msi_stats"]]
       # handle nulls
       msi <- msi %||% list(fracIndels = NA, predicted_class = NA)
       msi <- purrr::flatten(msi) |>
-        tibble::as_tibble() |>
+        tibble::as_tibble_row() |>
         dplyr::select("fracIndels", "predicted_class")
       metrics <- dplyr::bind_cols(msi, tmb)
       list(