test data were moved

R/data.r

@@ -5,10 +5,15 @@
 #'
 #' @format The full human model contains 22479 genes, associated pathways,
 #' p.value and p.adj value        
-#'
-#' @docType data
+#' \describe{
+#'     \item{gene}{gene names in HGNC symbols}
+#'     \item{pathway}{names of PROGENy pathways}
+#'     \item{weight}{z-scores for a given gene}
+#'     \item{p.value}{significance of gene in pathway}
+#' }
 #' @keywords datasets
 #' @name model_human_full
+#' @examples getFullModel("Human")
 #' @source \url{http://biorxiv.org/content/early/2016/08/28/065672}
 NULL
 
@@ -19,87 +24,14 @@ NULL
 #'
 #' @format The full mouse model contains 17426 genes, associated pathways,
 #' p.value and p.adj value
-#' 
-#' @docType data
+#' \describe{
+#'     \item{gene}{gene names in HGNC symbols}
+#'     \item{pathway}{names of PROGENy pathways}
+#'     \item{weight}{z-scores for a given gene}
+#'     \item{p.value}{significance of gene in a pathway}
+#' }
 #' @keywords datasets
 #' @name model_mouse_full
+#' @examples getFullModel("Mouse")
 #' @source \url{http://biorxiv.org/content/early/2016/08/28/065672}
 NULL
-
-#' The test human gene expression data
-#'
-#' HGNC gene symbols in rows, gene expression counts in columns.
-#'
-#' @format The test human gene expression data contains read counts info about 
-#' 121 genes in 8 conditions.
-#' 
-#' @docType data
-#' @keywords datasets
-#' @name input_human
-#' @source \url{http://biorxiv.org/content/early/2016/08/28/065672}
-NULL
-
-#' The test mouse gene expression data
-#'
-#' HGNC gene symbols in rows, gene expression counts in columns.
-#'
-#' @format The test mouse gene expression data contains read counts info about 
-#' 88 genes in 8 conditions.
-#' 
-#' @docType data
-#' @keywords datasets
-#' @name input_mouse
-#' @source \url{http://biorxiv.org/content/early/2016/08/28/065672}
-NULL
-
-#' The test human result output matrix produced by default progeny function
-#'
-#' Conditions in rows, pathways in columns.
-#'
-#' @format The test human result output matrix contains pathway score for each
-#' condtioin
-#' 
-#' @docType data
-#' @keywords datasets
-#' @name human_def_expected
-#' @source \url{http://biorxiv.org/content/early/2016/08/28/065672}
-NULL
-
-#' The test mouse result output matrix produced by default progeny function
-#'
-#' Conditions in rows, pathways in columns.
-#'
-#' @format The test mouse result output matrix contains pathway score for each
-#' condtioin
-#' 
-#' @docType data
-#' @keywords datasets
-#' @name mouse_def_expected
-#' @source \url{http://biorxiv.org/content/early/2016/08/28/065672}
-NULL
-
-#' The test human result output matrix produced by permutation progeny function
-#'
-#' Conditions in rows, pathways in columns.
-#'
-#' @format The test human result output matrix contains pathway score for each
-#' condtioin
-#' 
-#' @docType data
-#' @keywords datasets
-#' @name human_perm_expected
-#' @source \url{http://biorxiv.org/content/early/2016/08/28/065672}
-NULL
-
-#' The test mouse result output matrix produced by permutation progeny function
-#'
-#' Conditions in rows, pathways in columns.
-#'
-#' @format The test mouse result output matrix contains pathway score for each
-#' condtioin
-#' 
-#' @docType data
-#' @keywords datasets
-#' @name mouse_perm_expected
-#' @source \url{http://biorxiv.org/content/early/2016/08/28/065672}
-NULL