Improve doccumentation for fetch_deconvo_data

#8

R/fetch_deconvo_data.R

@@ -1,6 +1,14 @@
 
 
 #' Download Human DLPFC Deconvolution Data
+#' 
+#'  This function downloads from ExperimentHub, if ExperimentHub is not 
+#'  available, this function will download the files from Dropbox using 
+#'  BiocFileCache::bfcrpath() unless the files are present already at destdir. 
+#'  
+#'  Note that ExperimentHub and BiocFileCache will cache the data and 
+#'  automatically detect if you have previously downloaded it, thus making it 
+#'  the preferred way to interact with the data.
 #'
 #' @param type A `character(1)` specifying which file you want to download. 
 #' `rse_gene` {RangedSummarizedExperiment} with 110 bulk RNA-seq samples
@@ -14,15 +22,30 @@
 #' [BiocFileCache-class][BiocFileCache::BiocFileCache-class]. Used when
 #' `eh` is not available.
 #'
-#' @return The requested object
+#' @return The requested object: `rse_gene` that you assign to an object
 #' @export
 #' @import ExperimentHub
 #' @import BiocFileCache
 #' @importFrom AnnotationHub query
 #' @importFrom methods is
 #'
 #' @examples
-#' rse_gene <- fetch_deconvo_data("rse_gene")
+#' ## Download the bulk RNA gene expression data
+#' ## A RangedSummarizedExperiment (41.16 MB)
+#' 
+#' if (!exists("rse-gene")) rse_gene <- fetch_deconvo_data("rse_gene")
+#' 
+#' ## explore data
+#' rse_gene
+#' class: RangedSummarizedExperiment 
+#' # dim: 21745 110 
+#' # metadata(1): SPEAQeasy_settings
+#' # assays(2): counts logcounts
+#' # rownames(21745): ENSG00000227232.5 ENSG00000278267.1 ... ENSG00000210195.2 ENSG00000210196.2
+#' # rowData names(11): Length gencodeID ... gencodeTx passExprsCut
+#' # colnames(110): 2107UNHS-0291_Br2720_Mid_Bulk 2107UNHS-0291_Br2720_Mid_Cyto ... AN00000906_Br8667_Mid_Cyto
+#' # AN00000906_Br8667_Mid_Nuc
+#' # colData names(78): SAMPLE_ID Sample ... diagnosis qc_class
 #' 
 fetch_deconvo_data <- function(type = c("rse_gene"),
                              destdir = tempdir(),