add documentation for the output

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ermineR
 Title: Gene set analysis with multifunctionality assessment
-Version: 1.0.2.9000
+Version: 1.0.3.9000
 Authors@R: person("Ogan", "Mancarci", email = "[email protected]", role = c("aut", "cre"))
 Description: ErmineR is an interface to the ermineJ gene set analysis software (http://erminej.msl.ubc.ca). 
 Depends: R (>= 3.4.0)
@@ -26,4 +26,4 @@ Suggests:
     tools
 Remotes:
     PavlidisLab/gemma.R
-RoxygenNote: 7.2.1
+RoxygenNote: 7.3.2

R/ermineR.R

@@ -17,7 +17,26 @@
 #' @inheritParams geneSetOpts
 #' @inheritParams returnOpts
 #'
-#' @return A list
+#' @return A list containing a "results" component and a "details" component. 
+#' "results" is a data.frame containing the main output. The columns of this table are
+#' 
+#' \itemize{
+#'     \item \code{Name}: the name of the gene set
+#'     \item \code{ID}: the id of the gene set
+#'     \item \code{NumProbes}:  the number of elements (e.g. probes) in the gene set.
+#'     \item \code{NumGenes}: the number of genes in the gene set.
+#'     \item \code{RawScore}: the raw statistic for the gene set. For explanations see this page
+#'     \item \code{Pval}: the p value for the gene set.
+#'     \item \code{CorrectedPvalue}: the corrected p pvalue. See this page for more information.
+#'     \item \code{MFPvalue}: pvalue after multifunctionality correction. Might be missing if correction was not performed.
+#'     \item \code{CorrectedMFPvalue}: Like CorrectedPvalue, but for the multifunctionality “corrected” pvalue.
+#'     \item \code{Multifunctionality}: How biased the genes in the set are towards multifunctional genes.
+#'     \item \code{Same as}: a list of gene sets which have the exact same members as this one. Such gene sets are not listed anywhere else.
+#'     \item \code{GeneMembers}: If you selected the “Include genes” option when saving, this will contain a list of the genes that are in the gene set, separated by “|”.
+#' }
+#' 
+#' "details" section contain settings that were used to run the analysis.
+#' 
 #' @export
 #'
 ermineR = function(annotation = NULL, 

R/testWrappers.R

@@ -29,6 +29,9 @@
 #' @inheritParams generalStats
 #' @inheritParams geneSetOpts
 #' @inheritParams returnOpts
+#' 
+#' @inherit ermineR return
+#' 
 #' @export
 ora = function(scores = NULL,
                hitlist = NULL,
@@ -88,6 +91,8 @@ ora = function(scores = NULL,
 #' @inheritParams geneSetOpts
 #' @inheritParams returnOpts
 #' 
+#' @inherit ermineR return
+#' 
 #' @export
 gsr = function(scores,
                scoreColumn = 1,
@@ -143,6 +148,8 @@ gsr = function(scores,
 #' @inheritParams geneSetOpts
 #' @inheritParams returnOpts
 #' 
+#' @inherit ermineR return
+#' 
 #' @export
 precRecall = function(scores,
                       scoreColumn = 1,
@@ -204,6 +211,8 @@ precRecall = function(scores,
 #' @inheritParams geneSetOpts
 #' @inheritParams returnOpts
 #' 
+#' @inherit ermineR return
+#' 
 #' @export
 corr = function(expression,
                 annotation = NULL,
@@ -268,6 +277,8 @@ corr = function(expression,
 #' @inheritParams geneSetOpts
 #' @inheritParams returnOpts
 #' 
+#' @inherit ermineR return
+#' 
 #' @export
 roc = function(scores,
                scoreColumn = 1,