Reoxygenated, updated NEWS.

mimi3421 · May 25, 2019 · fd26236 · fd26236
1 parent 9e1fea0
commit fd26236
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Showing 4 changed files with 96 additions and 33 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -42,6 +42,7 @@ export(plotScater)
 export(plotTSNE)
 export(plotUMAP)
 export(readSparseCounts)
+export(runColDataPCA)
 export(runDiffusionMap)
 export(runMDS)
 export(runTSNE)
@@ -80,7 +81,6 @@ importFrom(BiocParallel,bplapply)
 importFrom(BiocParallel,bpmapply)
 importFrom(BiocParallel,bpnworkers)
 importFrom(BiocSingular,ExactParam)
-importFrom(BiocSingular,IrlbaParam)
 importFrom(BiocSingular,runPCA)
 importFrom(DelayedArray,DelayedArray)
 importFrom(DelayedArray,sweep)

diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
@@ -6,6 +6,8 @@
     \item Removed deprecated dplyr verbs.
     \item Removed deprecated method= option in runPCA().
     Increased ncomponents= default to 50.
+    Deprecated use_coldata= and related options in favour of runColDataPCA().
+    \item Added runColDataPCA() function for running PCA on colData().
     \item Pass all ... options to biomaRt::useMart() in getBMFeatureAnnos().
   }
 }

diff --git a/man/runColDataPCA.Rd b/man/runColDataPCA.Rd
diff --git a/man/runPCA.Rd b/man/runPCA.Rd