GHA: add telemetry

js2264 · Jun 27, 2023 · 9947741 · 9947741
1 parent 2f9308c
commit 9947741
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diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml
@@ -34,18 +34,15 @@ jobs:
           r: auto
           cont: bioconductor/bioconductor_docker:RELEASE_3_17
           rspm: https://packagemanager.rstudio.com/cran/__linux__/focal/release
-        # - os: macOS-latest
-        #   bioc: devel
-        #   r: auto
-        #   cont: ~
-        #   rspm: ~
         - os: windows-latest
           bioc: devel
           r: auto
           cont: ~
           rspm: ~
     steps:
     - uses: runforesight/workflow-telemetry-action@v1
+      with: 
+        github_token: ${{ secrets.GITHUB_TOKEN }}
     - uses: js2264/rworkflows@master
       with:
         run_bioccheck: ${{ true }}

diff --git a/GSE161259_ES_chr8_55400000_59200000_MAPQ30.40kb.cool b/GSE161259_ES_chr8_55400000_59200000_MAPQ30.40kb.cool
diff --git a/R/HiCExperiment-class.R b/R/HiCExperiment-class.R
@@ -377,6 +377,23 @@ makeHiCExperimentFromGInteractions <- function(gi) {
         pairsFile = pairsFile, 
         metadata = c(list(regions = bed), metadata)
     )
+
+    ## -- If imported data is all integers, run ICE and save `balanced`
+    s <- scores(x, 'count')
+    if (all(as.integer(s) == s)) {
+        if (requireNamespace("HiContacts", quietly = TRUE)) {
+            x <- HiContacts::normalize(x)
+            names(x@scores)[2] <- 'balanced'
+        }
+        else {
+            warning('Install `HiContacts` package (`BiocManager::install("HiContacts")`)\nto balance Hi-C data.')
+        }
+    }
+    else {
+        message("Imported data stored in `balanced` scores.")
+        names(x@scores)[1] <- 'balanced'
+    }
+
     methods::validObject(x)
     return(x)
 }