Merge remote-tracking branch 'upstream/master' into add-rerun-files

.circleci/config.yml

@@ -44,7 +44,7 @@ jobs:
 
       - run:
           name: Molecular subtyping - Non-MB/Non-ATRT Embryonal tumors
-          command: OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-embryonal/run-embryonal-subtyping.sh
+          command: OPENPBTA_TESTING=1 OPENPBTA_SUBSET=0 ./scripts/run_in_ci.sh bash analyses/molecular-subtyping-embryonal/run-embryonal-subtyping.sh
 
       - run:
           name: Molecular Subtyping and Plotting - ATRT

Dockerfile

@@ -415,6 +415,8 @@ RUN R -e "remotes::install_github('coolbutuseless/ggpattern', ref = '390e13fead0
 RUN ./install_bioc.r \
     ggforce
 
+RUN  R -e "remotes::install_github('d3b-center/medullo-classifier-package', ref = 'e3d12f64e2e4e00f5ea884f3353eb8c4b612abe8', dependencies = TRUE, upgrade = FALSE, force = TRUE)" \
+   && Rscript -e "library(medulloPackage)"
 
 #### Please install your dependencies immediately above this comment.
 #### Add a comment to indicate what analysis it is required for

analyses/molecular-subtyping-EWS/01-run-subtyping-ewings.Rmd

@@ -32,10 +32,7 @@ clinical <- readr::read_tsv(file.path(dataDir, "pbta-histologies-base.tsv"),
 
 # get ewings fusion calls from fusion-summary results file
 ewings_foi_bsids <- readr::read_tsv(
-  file.path(root_dir, 
-            "analyses",
-            "fusion-summary",
-            "results",
+  file.path(dataDir,
             "fusion_summary_ewings_foi.tsv")
   ) 
 
@@ -127,7 +124,3 @@ ews_subtype %>%
   readr::write_tsv(file.path(results_dir, "EWS_results.tsv"))
 ```
 
-
-
-
-

analyses/molecular-subtyping-EWS/01-run-subtyping-ewings.nb.html

@@ -1776,17 +1776,17 @@ <h4 class="date">January 2020</h4>
 <!-- rnb-source-begin eyJkYXRhIjoibGlicmFyeShcInRpZHl2ZXJzZVwiKSJ9 -->
 <pre class="r"><code>library(&quot;tidyverse&quot;)</code></pre>
 <!-- rnb-source-end -->
-<!-- rnb-message-begin eyJkYXRhIjoi4pSA4pSAIEF0dGFjaGluZyBwYWNrYWdlcyDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIAgdGlkeXZlcnNlIDEuMi4xIOKUgOKUgFxuIn0= -->
-<pre><code>── Attaching packages ────────────────────────────────── tidyverse 1.2.1 ──</code></pre>
+<!-- rnb-message-begin eyJkYXRhIjoi4pSA4pSAIEF0dGFjaGluZyBwYWNrYWdlcyDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIAgdGlkeXZlcnNlIDEuMi4xIOKUgOKUgFxuIn0= -->
+<pre><code>── Attaching packages ────────────────────────────────────────────────────────────────── tidyverse 1.2.1 ──</code></pre>
 <!-- rnb-message-end -->
 <!-- rnb-message-begin eyJkYXRhIjoi4pyUIGdncGxvdDIgMy4yLjAgICAgIOKclCBwdXJyciAgIDAuMy4yXG7inJQgdGliYmxlICAyLjEuMyAgICAg4pyUIGRwbHlyICAgMC44LjNcbuKclCB0aWR5ciAgIDAuOC4zICAgICDinJQgc3RyaW5nciAxLjQuMFxu4pyUIHJlYWRyICAgMS4zLjEgICAgIOKclCBmb3JjYXRzIDAuNC4wXG4ifQ== -->
 <pre><code>✔ ggplot2 3.2.0     ✔ purrr   0.3.2
 ✔ tibble  2.1.3     ✔ dplyr   0.8.3
 ✔ tidyr   0.8.3     ✔ stringr 1.4.0
 ✔ readr   1.3.1     ✔ forcats 0.4.0</code></pre>
 <!-- rnb-message-end -->
-<!-- rnb-message-begin eyJkYXRhIjoi4pSA4pSAIENvbmZsaWN0cyDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIAgdGlkeXZlcnNlX2NvbmZsaWN0cygpIOKUgOKUgFxu4pyWIGRwbHlyOjpmaWx0ZXIoKSBtYXNrcyBzdGF0czo6ZmlsdGVyKClcbuKcliBkcGx5cjo6bGFnKCkgICAgbWFza3Mgc3RhdHM6OmxhZygpXG4ifQ== -->
-<pre><code>── Conflicts ───────────────────────────────────── tidyverse_conflicts() ──
+<!-- rnb-message-begin eyJkYXRhIjoi4pSA4pSAIENvbmZsaWN0cyDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIDilIAgdGlkeXZlcnNlX2NvbmZsaWN0cygpIOKUgOKUgFxu4pyWIGRwbHlyOjpmaWx0ZXIoKSBtYXNrcyBzdGF0czo6ZmlsdGVyKClcbuKcliBkcGx5cjo6bGFnKCkgICAgbWFza3Mgc3RhdHM6OmxhZygpXG4ifQ== -->
+<pre><code>── Conflicts ───────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
 ✖ dplyr::filter() masks stats::filter()
 ✖ dplyr::lag()    masks stats::lag()</code></pre>
 <!-- rnb-message-end -->
@@ -1830,13 +1830,10 @@ <h3>Read in data</h3>
 <!-- rnb-message-begin eyJkYXRhIjoiU2VlIHNwZWMoLi4uKSBmb3IgZnVsbCBjb2x1bW4gc3BlY2lmaWNhdGlvbnMuXG4ifQ== -->
 <pre><code>See spec(...) for full column specifications.</code></pre>
 <!-- rnb-message-end -->
-<!-- rnb-source-begin eyJkYXRhIjpbIiMgZ2V0IGV3aW5ncyBmdXNpb24gY2FsbHMgZnJvbSBmdXNpb24tc3VtbWFyeSByZXN1bHRzIGZpbGUiLCJld2luZ3NfZm9pX2JzaWRzIDwtIHJlYWRyOjpyZWFkX3RzdihcbiAgZmlsZS5wYXRoKHJvb3RfZGlyLCBcbiAgICAgICAgICAgIFwiYW5hbHlzZXNcIixcbiAgICAgICAgICAgIFwiZnVzaW9uLXN1bW1hcnlcIixcbiAgICAgICAgICAgIFwicmVzdWx0c1wiLFxuICAgICAgICAgICAgXCJmdXNpb25fc3VtbWFyeV9ld2luZ3NfZm9pLnRzdlwiKVxuICApICJdfQ== -->
+<!-- rnb-source-begin eyJkYXRhIjpbIiMgZ2V0IGV3aW5ncyBmdXNpb24gY2FsbHMgZnJvbSBmdXNpb24tc3VtbWFyeSByZXN1bHRzIGZpbGUiLCJld2luZ3NfZm9pX2JzaWRzIDwtIHJlYWRyOjpyZWFkX3RzdihcbiAgZmlsZS5wYXRoKGRhdGFEaXIsXG4gICAgICAgICAgICBcImZ1c2lvbl9zdW1tYXJ5X2V3aW5nc19mb2kudHN2XCIpXG4gICkgIl19 -->
 <pre class="r"><code># get ewings fusion calls from fusion-summary results file
 ewings_foi_bsids &lt;- readr::read_tsv(
-  file.path(root_dir, 
-            &quot;analyses&quot;,
-            &quot;fusion-summary&quot;,
-            &quot;results&quot;,
+  file.path(dataDir,
             &quot;fusion_summary_ewings_foi.tsv&quot;)
   ) </code></pre>
 <!-- rnb-source-end -->
@@ -1968,7 +1965,7 @@ <h4>Save to file</h4>
 </div>
 </div>
 
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analyses/molecular-subtyping-MB/01-filter-and-batch-correction.R

@@ -31,8 +31,8 @@ dir.create(output_dir, showWarnings = FALSE, recursive = TRUE)
 
 # input files
 clin_file <- file.path(data_dir, "pbta-histologies-base.tsv")
-polya.file <- file.path(root_dir, "analyses", "collapse-rnaseq", "results", "pbta-gene-expression-rsem-fpkm-collapsed.polya.rds")
-stranded.file <- file.path(root_dir, "analyses", "collapse-rnaseq", "results","pbta-gene-expression-rsem-fpkm-collapsed.stranded.rds")
+polya.file <- file.path(root_dir, "data", "pbta-gene-expression-rsem-fpkm-collapsed.polya.rds")
+stranded.file <- file.path(root_dir, "data","pbta-gene-expression-rsem-fpkm-collapsed.stranded.rds")
 terms.file <- file.path("input", "mb_subtyping_path_dx_strings.json")
 
 # Read in the JSON file that contains the strings we'll use to include or

analyses/molecular-subtyping-MB/04-no-RNA-samples.R

@@ -10,17 +10,17 @@ suppressPackageStartupMessages({
 root_dir <- rprojroot::find_root(rprojroot::has_dir(".git"))
 
 # set results directory
-output_dir <- file.path(root_dir, "analyses", "molecular-subtyping-MB", "results") 
+output_dir <- file.path(root_dir, "analyses", "molecular-subtyping-MB", "results")
 dir.create(output_dir, showWarnings = FALSE, recursive = TRUE)
 
 # read medulloblastoma samples from histology
-mb_samples <- file.path(root_dir, "data", "pbta-histologies.tsv") %>%
+mb_samples <- file.path(root_dir, "data", "pbta-histologies-base.tsv") %>%
   read_tsv() %>%
-  filter(cancer_group == "Medulloblastoma",
+  filter(short_histology == "Medulloblastoma",
          sample_type == "Tumor")
 
 # samples where no RNA-Seq data is available
-sample_ids_with_rna <- mb_samples %>% 
+sample_ids_with_rna <- mb_samples %>%
   filter(experimental_strategy == "RNA-Seq")
 samples_ids_no_rna <- mb_samples %>%
   filter(!sample_id %in% sample_ids_with_rna$sample_id)