@@ -1,7 +1,7 @@

 Package: NoRCE

 Type: Package

 Title: NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment

-Version: 0.99.15

+Version: 0.99.16

 Authors@R: c(person("Gulden", "Olgun", 

            email = "gulden@cs.bilkent.edu.tr", 

 		   role = c("aut", "cre")))

@@ -10,7 +10,9 @@

 #' @importFrom ggplot2 ggplot

 #' @importFrom AnnotationDbi Term

 #'

-#'

+#' @examples

+#' ncGO <- geneGOEnricher(gene = brain_disorder_ncRNA[1:100,],

+#'   org_assembly='hg19', near=TRUE,  genetype = 'Ensembl_gene')

 #' 

 #' @export

 drawDotPlot <- function(mrnaObject, type = "pAdjust", n) {

@@ -85,7 +87,10 @@ drawDotPlot <- function(mrnaObject, type = "pAdjust", n) {

 #'

 #' @importFrom utils browseURL read.table write.table

 #'

-#'

+#' @examples

+#' ncGO <- geneGOEnricher(gene = brain_disorder_ncRNA[1:100,],

+#'   org_assembly='hg19', near=TRUE,  genetype = 'Ensembl_gene')

+#'   

 #' @export

 writeEnrichment <-

   function(mrnaObject,

@@ -122,7 +127,7 @@ writeEnrichment <-

 #'

 #' @return Give top n enrichment results

 #'

-#'

+#'   

 #' @export

 topEnrichment <- function(mrnaObject, type, n) {

   if (missing(mrnaObject)) {

@@ -241,6 +246,10 @@ topEnrichment <- function(mrnaObject, type, n) {

 #' @importFrom ggplot2 aes element_text geom_point ggplot labs theme theme_bw

 #'

 #'

+#' @examples

+#' ncGO <- geneGOEnricher(gene = brain_disorder_ncRNA[1:100,],

+#'   org_assembly='hg19', near=TRUE,  genetype = 'Ensembl_gene')

+#' 

 #' @export

 createNetwork <-

   function(mrnaObject,

@@ -375,7 +384,10 @@ createNetwork <-

 #' @importFrom png readPNG writePNG

 #' @importFrom RCurl postForm

 #'

-#'

+#' @examples

+#' ncGO <- geneGOEnricher(gene = brain_disorder_ncRNA[1:100,],

+#'   org_assembly='hg19', near=TRUE,  genetype = 'Ensembl_gene')

+#'   

 #' @export

 getGoDag <-

   function(mrnaObject,

@@ -39,3 +39,8 @@ Nodes are GO term and mRNA, edges are interactions between them. Each

 GO-term is annotated and enriched with the mRNAs provided from the input

 list.

 }

+\examples{

+ncGO <- geneGOEnricher(gene = brain_disorder_ncRNA[1:100,],

+  org_assembly='hg19', near=TRUE,  genetype = 'Ensembl_gene')

+

+}

@@ -21,3 +21,8 @@ Dot plot of the top n enrichment results

 \description{

 Draw dot plot of the enrichment object

 }

+\examples{

+ncGO <- geneGOEnricher(gene = brain_disorder_ncRNA[1:100,],

+  org_assembly='hg19', near=TRUE,  genetype = 'Ensembl_gene')

+

+}

@@ -30,3 +30,8 @@ Saves image file in a given format

 Plot and save the GO term DAG of the top n enrichments in terms of p-values

 or adjusted p-values with an user provided format

 }

+\examples{

+ncGO <- geneGOEnricher(gene = brain_disorder_ncRNA[1:100,],

+  org_assembly='hg19', near=TRUE,  genetype = 'Ensembl_gene')

+  

+}

@@ -26,3 +26,8 @@ Text file of the enrichment results in a tabular format

 \description{

 Write the tabular form of the pathway or GO term enrichment results

 }

+\examples{

+ncGO <- geneGOEnricher(gene = brain_disorder_ncRNA[1:100,],

+  org_assembly='hg19', near=TRUE,  genetype = 'Ensembl_gene')

+  

+}