simplify GLMPCA method definitions and set default assay to 'counts' …

…addresses #5 . Moves the L argument in front of assay since it is a required positional argument by glmpca

NAMESPACE

@@ -7,13 +7,11 @@ export(nullResiduals)
 exportMethods(GLMPCA)
 exportMethods(devianceFeatureSelection)
 exportMethods(nullResiduals)
-import(glmpca)
 importFrom(Matrix,t)
 importFrom(SingleCellExperiment,"reducedDim<-")
 importFrom(SummarizedExperiment,"assay<-")
 importFrom(SummarizedExperiment,"rowData<-")
 importFrom(SummarizedExperiment,assay)
 importFrom(SummarizedExperiment,rowData)
-importFrom(glmpca,glmpca)
 importFrom(methods,as)
 importFrom(methods,is)

R/AllGenerics.R

@@ -4,7 +4,7 @@
 #'   methods.
 #' @export
 setGeneric(
-    name = "devianceFeatureSelection",     #signature = 'object',
+    name = "devianceFeatureSelection", 
     def = function(object, ...) {
         standardGeneric("devianceFeatureSelection")
     }
@@ -18,7 +18,6 @@ setGeneric(
 #' @export
 setGeneric(
     name = "GLMPCA",
-    signature = 'object',
     def = function(object, ...) {
         standardGeneric("GLMPCA")
     }

R/glmpca.R

@@ -5,11 +5,11 @@
 #'   \code{\link[glmpca]{glmpca}}.
 #' 
 #' @param object A \code{\link{SingleCellExperiment}} or
-#'   \link{SummarizedExperiment} object. Alternatively, a matrix of integer
-#'   counts.
-#' @param assay a character or integer specifying which assay to use for GLM-PCA
-#'   (default = 1). Ignored if \code{object} is a matrix.
+#'   \link{SummarizedExperiment} object. Alternatively, a matrix-like object
+#'   of non-negative integer counts (such as a sparse \code{\link{Matrix}}).
 #' @param L the desired number of latent dimensions (integer).
+#' @param assay a character or integer specifying which assay to use for GLM-PCA
+#'   (default = 'counts'). Ignored if \code{object} is a matrix.
 #' @param ... further arguments passed to \code{\link[glmpca]{glmpca}}
 #'
 #' @return The original \code{SingleCellExperiment} or
@@ -26,35 +26,28 @@
 #' sce <- SingleCellExperiment::SingleCellExperiment(assays=list(counts=u))
 #' GLMPCA(sce, L = 2)
 #' 
-#' @import glmpca
 #' @importFrom SingleCellExperiment reducedDim<-
 #' @importFrom methods is
 #' @export
-setMethod(f = "GLMPCA",
-          signature = signature(object = "SummarizedExperiment"),
-          definition = function(object, assay = 1, L, ...){
-              res <- glmpca(Y = assay(object, assay), L = L, ...)
+setMethod(f = "GLMPCA","SummarizedExperiment",
+          definition = function(object, L, assay = "counts", ...){
+              res <- glmpca::glmpca(Y = assay(object, assay), L = L, ...)
               if(is(object, 'SingleCellExperiment')){
                   reducedDim(object, "GLMPCA") <- res$factors
               }
               object@metadata$glmpca <- res
               return(object)
           })
 
+#this function is only needed because the glmpca signature has "Y" not "object"
+glmpca_wrapper<-function(object, L, ...){
+    glmpca::glmpca(object, L, ...)
+}
+
 #' @rdname GLMPCA
-#' @importFrom glmpca glmpca
 #' @export
-setMethod(f = "GLMPCA",
-          signature = signature(object = "matrix"),
-          definition = function(object, assay = 1, L, ...){
-              glmpca(Y = object, L = L, ...)
-          })
+setMethod(f = "GLMPCA", "matrix", definition=glmpca_wrapper)
 
 #' @rdname GLMPCA
-#' @importFrom glmpca glmpca
 #' @export
-setMethod(f = "GLMPCA",
-          signature = signature(object = "Matrix"),
-          definition = function(object, assay = 1, L, ...){
-              glmpca(Y = object, L = L, ...)
-          })
+setMethod(f = "GLMPCA", "Matrix", definition=glmpca_wrapper)

tests/testthat/test-glmpca.R

@@ -1,12 +1,12 @@
 context("Test GLMPCA")
+require(SingleCellExperiment)
 set.seed(1234)
 
 test_that("GLMPCA works", {
     ncells <- 100
     u <- matrix(rpois(2000, 5), ncol=ncells)
     v <- log2(u + 1)
 
-    require(SingleCellExperiment)
     se <- SummarizedExperiment(assays=list(counts=u, logcounts=v))
     sce <- SingleCellExperiment(assays=list(counts=u, logcounts=v))