ds.acme changes

Author: Leire Abarrategui Martinez

NAMESPACE

@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 export(ds.Boole)
+export(ds.acme)
 export(ds.asCharacter)
 export(ds.asDataMatrix)
 export(ds.asFactor)

R/ds.acme.R

@@ -0,0 +1,53 @@
+#'
+#' @title ds.acme function template
+#' @description example aggregate function template
+#' @details Client-side acme example aggregate function template
+#' This file is to be placed in server-sides R directory.
+#' @param name a character vector containing "a name"
+#' @param datasources specifies the particular 'connection object(s)' to use.
+#' @return character vector containing "a message"
+#' @author Ever, Who.
+#' @export
+#'
+
+ds.acme <- function(model, Set, type.data = "SummarizedExperiment", threshold = NULL, 
+                    reference = NULL, annotCols=NULL, datasources=NULL)
+{   
+    # if no opal login details are provided look for 'opal' objects in the environment
+    if (is.null(datasources))
+    {
+        datasources <-  DSI::datashield.connections_find()
+    }
+    type <- charmatch(type.data, c("SummarizedExperiment", "matrix", "htseq"))
+  
+    if(is.na(type))
+    {
+       stop("type.data must be 'SummarizedExperiment', 'matrix', 'htseq'")
+    }
+    
+    mt <- all.vars(model)
+    variable_names <- mt[1] 
+    
+    if (length(mt)>1)
+    {
+      covariable_names <- paste(mt[-1], collapse=",")
+    }
+    
+    else
+    {
+      covariable_names <- NULL
+    }
+    
+    if (!is.null(annotCols))
+    {
+      annotCols <- paste(annotCols, collapse=",")
+    }
+
+    # call the server side function
+    calltext <- call("acmeDS",Set, type,variable_names, covariable_names, annotCols, threshold, reference)
+
+    output <- datashield.aggregate(datasources, calltext)
+  
+    return(output)
+}
+#ds.acme