Set iteration default to 10000. Clarify suggested iteration values in…

… docs

R/commonArguments.R

@@ -97,13 +97,17 @@ expression = function(expression){}
 
 #' iterations
 #' 
-#' @keywords internal GSR CORR
+#' @keywords internal GSR CORR precRecall
 #' 
 #' @name iterations
 #' 
-#' @param iterations Number of iterations (test = GSR and CORR methods only)
+#' @param iterations Number of iterations. We suggest a starting value of 10000 
+#' iterations. When you decide on parameters you like, we recommend a larger
+#' number of iterations (perhaps 200,000 or more). This is to get sufficient
+#' precision in the p-values to make multiple-test correction work correctly. 
+#' (test = GSR CORR and precRecall methods only)
 #' 
-iterations = function(iterations){}
+iterations = function(iterations = 10000){}
 
 #' generalStats
 #' 

R/ontology.R

@@ -6,10 +6,7 @@
 #' @param path File path. Without gz extension
 #' @param overwrite If TRUE, overwrites existing file
 #'
-#' @return
 #' @export
-#'
-#' @examples
 goToday = function(path,overwrite = FALSE){
     if(exists(path) & !overwrite){
         stop('File exists, not downloading')
@@ -46,7 +43,6 @@ getGoDates = function(){
 #' @param date Character. A valid date as returned from \code{\link{getGoDates}}.
 #' @param overwrite If TRUE, overwrites existing file
 #'
-#' @return
 #' @export
 goAtDate = function(path, date, overwrite = FALSE){
     if(exists(path)){

R/testWrappers.R

@@ -95,7 +95,7 @@ gsr = function(scores,
                logTrans = FALSE,
                annotation = NULL,
                aspects = c('Molecular Function','Cellular Component', 'Biological Process'),
-               iterations,
+               iterations = 10000,
                geneReplicates = c('mean','best'),
                pAdjust = c('FDR','Bonferroni'),
                geneSetDescription = 'Latest_GO',
@@ -150,7 +150,7 @@ precRecall = function(scores,
                       logTrans = FALSE,
                       annotation = NULL,
                       aspects = c('Molecular Function','Cellular Component', 'Biological Process'),
-                      iterations,
+                      iterations = 10000,
                       geneReplicates = c('mean','best'),
                       pAdjust =c('FDR','Bonferroni'),
                       geneSetDescription = 'Latest_GO',
@@ -208,7 +208,7 @@ precRecall = function(scores,
 corr = function(expression,
                 annotation = NULL,
                 aspects = c('Molecular Function','Cellular Component', 'Biological Process'),
-                iterations,
+                iterations = 10000,
                 geneReplicates = c('mean','best'),
                 pAdjust = c('FDR','Bonferroni'),
                 geneSetDescription = 'Latest_GO',