Improve Joint-RPCA

.gitignore

@@ -10,8 +10,3 @@
 docs/
 .DS_Store
 mia.BiocCheck/
-src/*.dll
-inst/extdata/taxonomic_profiles_mgx.tsv
-inst/extdata/ecs_relab.tsv
-inst/extdata/hmp2_metadata_2018-08-20.csv
-tools/cache/

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: mia
 Type: Package
-Version: 1.19.5
+Version: 1.19.6
 Authors@R:
     c(person(given = "Tuomas", family = "Borman", role = c("aut", "cre"),
              email = "tuomas.v.borman@utu.fi",

NAMESPACE

@@ -13,6 +13,7 @@ export(addDissimilarity)
 export(addDivergence)
 export(addDominant)
 export(addHierarchyTree)
+export(addJointRPCA)
 export(addLDA)
 export(addMDS)
 export(addMediation)
@@ -24,6 +25,7 @@ export(addPerSampleDominantTaxa)
 export(addPrevalence)
 export(addPrevalentAbundance)
 export(addRDA)
+export(addRPCA)
 export(addTaxonomyTree)
 export(agglomerateByModule)
 export(agglomerateByPrevalence)
@@ -85,6 +87,7 @@ export(getPrevalentAbundance)
 export(getPrevalentFeatures)
 export(getPrevalentTaxa)
 export(getRDA)
+export(getRPCA)
 export(getRare)
 export(getRareFeatures)
 export(getRareTaxa)
@@ -183,6 +186,7 @@ exportMethods(addDissimilarity)
 exportMethods(addDivergence)
 exportMethods(addDominant)
 exportMethods(addHierarchyTree)
+exportMethods(addJointRPCA)
 exportMethods(addLDA)
 exportMethods(addMDS)
 exportMethods(addMediation)
@@ -194,6 +198,7 @@ exportMethods(addPerSampleDominantTaxa)
 exportMethods(addPrevalence)
 exportMethods(addPrevalentAbundance)
 exportMethods(addRDA)
+exportMethods(addRPCA)
 exportMethods(addTaxonomyTree)
 exportMethods(agglomerateByModule)
 exportMethods(agglomerateByPrevalence)
@@ -235,6 +240,7 @@ exportMethods(getDominant)
 exportMethods(getExperimentCrossAssociation)
 exportMethods(getExperimentCrossCorrelation)
 exportMethods(getHierarchyTree)
+exportMethods(getJointRPCA)
 exportMethods(getLDA)
 exportMethods(getLowAbundant)
 exportMethods(getMDS)
@@ -249,6 +255,7 @@ exportMethods(getPrevalentAbundance)
 exportMethods(getPrevalentFeatures)
 exportMethods(getPrevalentTaxa)
 exportMethods(getRDA)
+exportMethods(getRPCA)
 exportMethods(getRare)
 exportMethods(getRareFeatures)
 exportMethods(getRareTaxa)
@@ -358,6 +365,7 @@ importFrom(MatrixGenerics,rowSums2)
 importFrom(MultiAssayExperiment,ExperimentList)
 importFrom(MultiAssayExperiment,MultiAssayExperiment)
 importFrom(MultiAssayExperiment,experiments)
+importFrom(MultiAssayExperiment,intersectColumns)
 importFrom(MultiAssayExperiment,sampleMap)
 importFrom(Rcpp,evalCpp)
 importFrom(Rcpp,sourceCpp)
@@ -435,6 +443,7 @@ importFrom(stats,chisq.test)
 importFrom(stats,cmdscale)
 importFrom(stats,cor)
 importFrom(stats,cor.test)
+importFrom(stats,dist)
 importFrom(stats,formula)
 importFrom(stats,gaussian)
 importFrom(stats,glm)

R/AllGenerics.R

@@ -410,3 +410,23 @@ setGeneric("addMDS", signature = "x", function(x, ...)
 #' @export
 setGeneric("getReducedDimAttribute", signature = "x", function(x, ...)
     standardGeneric("getReducedDimAttribute"))
+
+#' @rdname getRPCA
+#' @export
+setGeneric("getRPCA", signature = "x", function(x, ...)
+    standardGeneric("getRPCA"))
+
+#' @rdname getRPCA
+#' @export
+setGeneric("addRPCA", signature = "x", function(x, ...)
+    standardGeneric("addRPCA"))
+
+#' @rdname getRPCA
+#' @export
+setGeneric("getJointRPCA", signature = "x", function(x, ...)
+    standardGeneric("getJointRPCA"))
+
+#' @rdname getRPCA
+#' @export
+setGeneric("addJointRPCA", signature = "x", function(x, ...)
+    standardGeneric("addJointRPCA"))

R/cluster.R

@@ -104,7 +104,7 @@ setMethod("addCluster", signature = c(x = "SummarizedExperiment"),
         #
         result <- getCluster(
             x = x, BLUSPARAM = BLUSPARAM, assay.type = assay.type,
-            dimred = dimred, by = by, full = full, ...)
+            by = by, full = full, ...)
         # If user has specified full=TRUE, result includes additional info
         # that will be stored to metadata.
         if( full ){