Merge pull request #92 from andrearaithel/OHT

Optimal Hard Thresholding to determine optimal encoding dimension

.github/workflows/check-bioc.yml

@@ -53,10 +53,10 @@ jobs:
       matrix:
         config:
           # This needs to be updated after each Bioconductor release. Please make sure we have the matching R and Bioc versions in it. 
-          - { os: ubuntu-latest, r: '4.3', bioc: '3.18', cont: "bioconductor/bioconductor_docker:RELEASE_3_18", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: ubuntu-latest, r: 'next', bioc: '3.19', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: '4.3', bioc: '3.18'}
-          - { os: windows-latest, r: '4.3', bioc: '3.18'}
+          - { os: ubuntu-latest, r: '4.4', bioc: '3.20', cont: "bioconductor/bioconductor_docker:RELEASE_3_20", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: ubuntu-latest, r: 'next', bioc: '3.21', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: macOS-latest, r: '4.4', bioc: '3.20'}
+          - { os: windows-latest, r: '4.4', bioc: '3.20'}
           ## Check https://github.com/r-lib/actions/tree/master/examples
           ## for examples using the http-user-agent
     env:
@@ -81,7 +81,7 @@ jobs:
       ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
       ## If they update their steps, we will also need to update ours.
       - name: Checkout Repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       ## R is already included in the Bioconductor docker images
       - name: Setup R from r-lib

DESCRIPTION

@@ -77,7 +77,9 @@ Imports:
     tibble,
     tools,
     utils,
-    VGAM
+    VGAM,
+    RMTstat,
+    pracma
 Suggests:
     magick,
     BiocStyle,

NAMESPACE

@@ -44,6 +44,7 @@ export(createTestFraserSettings)
 export(currentType)
 export(deltaPsiValue)
 export(dontWriteHDF5)
+export(estimateBestQ)
 export(featureExclusionMask)
 export(filterExpression)
 export(filterExpressionAndVariability)
@@ -62,7 +63,6 @@ export(mergeCounts)
 export(mergeExternalData)
 export(name)
 export(nonSplicedReads)
-export(optimHyperParams)
 export(pVals)
 export(padjVals)
 export(pairedEnd)

R/Fraser-pipeline.R

@@ -26,7 +26,7 @@
 #'
 #' @inheritParams countRNA
 #' @param q The encoding dimensions to be used during the fitting proceadure.
-#'         Should be fitted using \code{\link{optimHyperParams}} if unknown.
+#'         Should be fitted using \code{\link{estimateBestQ}} if unknown.
 #'         If a named vector is provided it is used for the different
 #'         splicing types.
 #' @param implementation The method that should be used to correct for