@@ -23,6 +23,7 @@

 #'

 #' @examples

 #'

+#' \dontrun{

 #'    PathFiles<-system.file('extdata',package='EventPointer')

 #'    DONSON_GTF<-paste(PathFiles,'/DONSON.gtf',sep='')

 #'    PSRProbes<-paste(PathFiles,'/PSR_Probes.txt',sep='')

@@ -52,6 +53,8 @@

 #'                   PathGTF=Directory,

 #'                  EventsFile= EventsFound,

 #'                  microarray='HTA-2_0')

+#'                  

+#' }

 #'

 #' @export

@@ -13,7 +13,7 @@

 #' events.

 #'

 #' @examples

-#'

+#' \dontrun{

 #'   data(AllEvents_RNASeq)

 #'   data(SG_RNASeq)

 #'

@@ -28,6 +28,7 @@

 #'    EventsTxt<-paste(system.file('extdata',package='EventPointer'),'/EventsFound_RNASeq.txt',sep='')

 #'    PathGTF<-tempdir()

 #'    EventPointer_RNASeq_IGV(Events,SG_RNASeq,EventsTxt,PathGTF)

+#'    }

 #' @export

@@ -17,6 +17,7 @@

 #'

 #'

 #' @examples

+#' \dontrun{

 #'    data(EventXtrans)

 #'    data(PSIss)

 #'    # Design and contrast matrix:

@@ -30,6 +31,7 @@

 #'    Fit <- EventPointer_RNASeq_TranRef(Count_Matrix =  PSIss$ExpEvs,

 #'                                       Statistic = 'LogFC',Design = Design,

 #'                                       Contrast = Contrast)

+#' }

 #'

 #'

 #' @export

@@ -12,6 +12,7 @@

 #'  and the p.values for each contrast, and a third element (LocalFDR) with the information of the local false discovery rate.

 #'

 #' @examples

+#' \dontrun{

 #'       data(ArraysData)

 #'       PSI_Arrays_list<-EventPointer:::getPSI(ArraysData)

 #'       PSI_Arrays <- PSI_Arrays_list$PSI

@@ -21,6 +22,7 @@

 #'       # Statistical analysis:

 #'       

 #'       table <- PSI_Statistic(PSI_Arrays,Design = Design, Contrast = Contrast, nboot = 50)

+#'  }

 #'       

 #'

 #' @export

@@ -20,7 +20,7 @@

 #'  

 #' 

 #' @examples 

-#' 

+#' \dontrun{

 #'    data("EventXtrans")

 #'    data("TxD")

 #'    data("Fit")

@@ -33,6 +33,7 @@

 #'    Result_PDEA <- Protein_Domain_Enrichment(PathsxTranscript = EventXtrans,

 #'                                             TxD = TxD,

 #'                                             Diff_PSI = Fit$deltaPSI)

+#'    }

 #' 

 #' @export

 #' @import Matrix

@@ -48,6 +48,7 @@ Generates of files to be loaded in IGV for visualization and interpretation of e

 }

 \examples{

+\dontrun{

    PathFiles<-system.file('extdata',package='EventPointer')

    DONSON_GTF<-paste(PathFiles,'/DONSON.gtf',sep='')

    PSRProbes<-paste(PathFiles,'/PSR_Probes.txt',sep='')

@@ -77,5 +78,7 @@ Generates of files to be loaded in IGV for visualization and interpretation of e

                   PathGTF=Directory,

                  EventsFile= EventsFound,

                  microarray='HTA-2_0')

+                 

+}

 }

@@ -24,7 +24,7 @@ events.

 Generates of files to be loaded in IGV for visualization and interpretation of events

 }

 \examples{

-

+\dontrun{

   data(AllEvents_RNASeq)

   data(SG_RNASeq)

@@ -39,4 +39,5 @@ Generates of files to be loaded in IGV for visualization and interpretation of e

    EventsTxt<-paste(system.file('extdata',package='EventPointer'),'/EventsFound_RNASeq.txt',sep='')

    PathGTF<-tempdir()

    EventPointer_RNASeq_IGV(Events,SG_RNASeq,EventsTxt,PathGTF)

+   }

 }

@@ -32,6 +32,7 @@ of contrast and all these data.frame are sotred in an unique list.

 Statistical analysis of alternative splicing events with the output of GetPSI_FromTranRef

 }

 \examples{

+\dontrun{

    data(EventXtrans)

    data(PSIss)

    # Design and contrast matrix:

@@ -45,6 +46,7 @@ Statistical analysis of alternative splicing events with the output of GetPSI_Fr

    Fit <- EventPointer_RNASeq_TranRef(Count_Matrix =  PSIss$ExpEvs,

                                       Statistic = 'LogFC',Design = Design,

                                       Contrast = Contrast)

+}

 }

@@ -24,6 +24,7 @@ Statistical analysis of the alternative splicing events. This function takes as

 Perform a statistical analysis based on permutation test

 }

 \examples{

+\dontrun{

       data(ArraysData)

       PSI_Arrays_list<-EventPointer:::getPSI(ArraysData)

       PSI_Arrays <- PSI_Arrays_list$PSI

@@ -33,6 +34,7 @@ Perform a statistical analysis based on permutation test

       # Statistical analysis:

       table <- PSI_Statistic(PSI_Arrays,Design = Design, Contrast = Contrast, nboot = 50)

+ }

 }

@@ -30,7 +30,7 @@ A list containing the results of the protein domain enrichment anaylisis. This l

 Analyze whether the presence of a protein domain increases or decreases in the condition under study.

 }

 \examples{

-

+\dontrun{

    data("EventXtrans")

    data("TxD")

    data("Fit")

@@ -43,5 +43,6 @@ Analyze whether the presence of a protein domain increases or decreases in the c

    Result_PDEA <- Protein_Domain_Enrichment(PathsxTranscript = EventXtrans,

                                             TxD = TxD,

                                             Diff_PSI = Fit$deltaPSI)

+   }

 }