adds runnable examples, adds news, adds description text

DESCRIPTION

@@ -4,7 +4,7 @@ Title: Framework for cell size scale factor normalized bulk transcriptomics deco
 Authors@R: c(person(c("Sean", "K"), "Maden", role = c("cre", "aut"), 
     email = "maden.sean@gmail.com", comment = c(ORCID = "0000-0002-2212-4894")),
     person("Stephanie", "Hicks", role = "aut", email = "shicks19@gmail.com", comment = c(ORCID = "0000-0002-7858-0231")))
-Description: Resources for deconvolution experiments and standard application of cell size scale factor normalizations. Includes specific object classes and extensible generics for deconvolution and cell type marker selection algorithms.
+Description: Provides a framework for adjustment on cell type size when performing bulk transcripomics deconvolution. The main framework function provides a means of reference normalization using cell size scale factors. It allows for marker selection and deconvolution using non-negative least squares (NNLS) by default. The framework is extensible for other marker selection and deconvolution algorithms, and users may reuse the generics, methods, and classes for these when developing new algorithms.
 License: Artistic-2.0
 Encoding: UTF-8
 URL: https://github.com/metamaden/lute
@@ -39,7 +39,7 @@ Suggests:
     DelayedArray
 VignetteBuilder:
     knitr
-biocViews: RNASeq, Sequencing, SingleCell, Coverage
+biocViews: RNASeq, Sequencing, SingleCell, Coverage, Transcriptomics
 RoxygenNote: 7.2.3
 Collate: 
     'lute_generics.R'

NEWS.Rd

@@ -0,0 +1,8 @@
+\name{NEWS}
+\title{News for Package \pkg{lute}}
+
+\section{Changes in version 0.99.0, Bioconductor 3.18 Release}{
+  \itemize{
+    \item Add \pkg{testthat} unit tests.
+  }
+}

R/findmarkersParam-class.R

@@ -55,6 +55,13 @@ setClass("findmarkersParam", contains="typemarkersParam",
 #' @details Main class for mapping arguments to the findMarkers method 
 #' implemented as \code{scran::findMarkers()}.
 #' 
+#' @examples 
+#' lexample <- get_decon_example_data()
+#' sce.example <- random_sce()
+#' new.param <- findmarkersParam(sce = sce.example, 
+#' celltype.variable = "celltype", markers.per.type = 5)
+#' markers <- typemarkers(new.param)
+#' 
 #' @export
 findmarkersParam <- function(sce, assay.name = "counts", 
                              celltype.variable = "cellType",
@@ -79,6 +86,13 @@ findmarkersParam <- function(sce, assay.name = "counts",
 #' 
 #' @importFrom scran findMarkers
 #' @importFrom dplyr %>%
+#' 
+#' @examples 
+#' lexample <- get_decon_example_data()
+#' sce.example <- random_sce()
+#' new.param <- findmarkersParam(sce = sce.example, 
+#' celltype.variable = "celltype", markers.per.type = 5)
+#' markers <- typemarkers(new.param)
 #'
 #' @returns Returns the top available markers, with type-specific marker filters,
 #' as either a vector of marker IDs or a results list.

R/lute_metadata.R

@@ -13,6 +13,9 @@
 #'
 #' @importFrom utils read.csv
 #' 
+#' @examples
+#' lute_supported_deconvolution_algorithms()
+#' 
 #' @export
 lute_supported_deconvolution_algorithms <- function(){
   csv.name <- "lute-deconvolution_transfer-learning-table.csv"