@@ -44,6 +44,7 @@ recommended to have at least 1.5 GB of free space.

 Generates the CDF file to be used under the aroma.affymetrix framework.

 }

 \examples{

+ \dontrun{

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

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

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

@@ -55,5 +56,6 @@ Generates the CDF file to be used under the aroma.affymetrix framework.

    CDFfromGTF_Multipath(input='AffyGTF',inputFile=DONSON_GTF,PSR=PSRProbes,Junc=JunctionProbes,

                         PathCDF=Directory,microarray=microarray,paths=3)

+ }

 }

@@ -4,8 +4,15 @@

 \alias{CDFfromGTF_Multipath}

 \title{CDF file creation for EventPointer (MultiPath)}

 \usage{

-CDFfromGTF_Multipath(input = "Ensembl", inputFile = NULL, PSR, Junc,

-  PathCDF, microarray = NULL, paths = 2)

+CDFfromGTF_Multipath(

+  input = "Ensembl",

+  inputFile = NULL,

+  PSR,

+  Junc,

+  PathCDF,

+  microarray = NULL,

+  paths = 2

+)

 }

 \arguments{

 \item{input}{Reference transcriptome used to build the CDF file. Must be one of Ensembl,

@@ -2,7 +2,7 @@

 % Please edit documentation in R/CDFfromGTF_Multipath.R

 \name{CDFfromGTF_Multipath}

 \alias{CDFfromGTF_Multipath}

-\title{CDF file creation for EventPointer}

+\title{CDF file creation for EventPointer (MultiPath)}

 \usage{

 CDFfromGTF_Multipath(input = "Ensembl", inputFile = NULL, PSR, Junc,

   PathCDF, microarray = NULL, paths = 2)

@@ -26,7 +26,7 @@ ClariomD, RTA or MTA}

 }

 \value{

 The function displays a progress bar to show the user the progress of the function.

-However, there is no value returned in R as the function creates three files that are used 

+However, there is no value returned in R as the function creates three files that are used

 later by other EventPointer functions. 1) EventsFound.txt : Tab separated file with all

 the information of all the alternative splcing events found. 2) .flat file : Used to build

 the corresponding CDF file. 3) .CDF file: Output required for the aroma.affymetrix preprocessing

@@ -34,7 +34,7 @@ pipeline. Both the .flat and .CDF file take large ammounts of memory in the hard

 recommended to have at least 1.5 GB of free space.

 }

 \description{

-Generates the CDF file to be used under the aroma.affymetrix framework

+Generates the CDF file to be used under the aroma.affymetrix framework.

 }

 \examples{

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

@@ -42,7 +42,7 @@ Generates the CDF file to be used under the aroma.affymetrix framework

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

    JunctionProbes<-paste(PathFiles,'/Junction_Probes.txt',sep='')

    Directory<-tempdir()

-   microarray<-"HTA-2_0"

+   microarray<-'HTA-2_0'

   # Run the function

@@ -8,7 +8,8 @@ CDFfromGTF_Multipath(input = "Ensembl", inputFile = NULL, PSR, Junc,

   PathCDF, microarray = NULL, paths = 2)

 }

 \arguments{

-\item{input}{Reference transcriptome used to build the CDF file. Must be one of Ensembl, UCSC or GTF.}

+\item{input}{Reference transcriptome used to build the CDF file. Must be one of Ensembl,

+UCSC or GTF.}

 \item{inputFile}{If input is GTF, inputFile should point to the GTF file to be used.}

@@ -18,15 +19,18 @@ CDFfromGTF_Multipath(input = "Ensembl", inputFile = NULL, PSR, Junc,

 \item{PathCDF}{Directory where the output will be saved}

-\item{microarray}{Microarray used to create the CDF file. Must be one of: HTA-2_0, ClariomD, RTA or MTA}

+\item{microarray}{Microarray used to create the CDF file. Must be one of: HTA-2_0,

+ClariomD, RTA or MTA}

 \item{paths}{Maximum number of paths of the events to find.}

 }

 \value{

-The function displays a progress bar to show the user the progress of the function. However, there is no value returned in R as

-the function creates three files that are used later by other EventPointer functions. 1) EventsFound.txt : Tab separated file with all

-the information of all the alternative splcing events found. 2) .flat file : Used to build the corresponding CDF file. 3) .CDF file: Output

-required for the aroma.affymetrix preprocessing pipeline. Both the .flat and .CDF file take large ammounts of memory in the hard drive, it is

+The function displays a progress bar to show the user the progress of the function.

+However, there is no value returned in R as the function creates three files that are used 

+later by other EventPointer functions. 1) EventsFound.txt : Tab separated file with all

+the information of all the alternative splcing events found. 2) .flat file : Used to build

+the corresponding CDF file. 3) .CDF file: Output required for the aroma.affymetrix preprocessing

+pipeline. Both the .flat and .CDF file take large ammounts of memory in the hard drive, it is

 recommended to have at least 1.5 GB of free space.

 }

 \description{

@@ -42,6 +46,7 @@ Generates the CDF file to be used under the aroma.affymetrix framework

   # Run the function

-   CDFfromGTF_Multipath(input='AffyGTF',inputFile=DONSON_GTF,PSR=PSRProbes,Junc=JunctionProbes,PathCDF=Directory,microarray=microarray,paths=3)

+   CDFfromGTF_Multipath(input='AffyGTF',inputFile=DONSON_GTF,PSR=PSRProbes,Junc=JunctionProbes,

+                        PathCDF=Directory,microarray=microarray,paths=3)

 }

@@ -42,6 +42,6 @@ Generates the CDF file to be used under the aroma.affymetrix framework

   # Run the function

-   CDFfromGTF_Multipath(input='GTF',inputFile=DONSON_GTF,PSR=PSRProbes,Junc=JunctionProbes,PathCDF=Directory,microarray=microarray,paths=3)

+   CDFfromGTF_Multipath(input='AffyGTF',inputFile=DONSON_GTF,PSR=PSRProbes,Junc=JunctionProbes,PathCDF=Directory,microarray=microarray,paths=3)

 }

new file mode 100644

@@ -0,0 +1,47 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/CDFfromGTF_Multipath.R

+\name{CDFfromGTF_Multipath}

+\alias{CDFfromGTF_Multipath}

+\title{CDF file creation for EventPointer}

+\usage{

+CDFfromGTF_Multipath(input = "Ensembl", inputFile = NULL, PSR, Junc,

+  PathCDF, microarray = NULL, paths = 2)

+}

+\arguments{

+\item{input}{Reference transcriptome used to build the CDF file. Must be one of Ensembl, UCSC or GTF.}

+

+\item{inputFile}{If input is GTF, inputFile should point to the GTF file to be used.}

+

+\item{PSR}{Path to the Exon probes txt file}

+

+\item{Junc}{Path to the Junction probes txt file}

+

+\item{PathCDF}{Directory where the output will be saved}

+

+\item{microarray}{Microarray used to create the CDF file. Must be one of: HTA-2_0, ClariomD, RTA or MTA}

+

+\item{paths}{Maximum number of paths of the events to find.}

+}

+\value{

+The function displays a progress bar to show the user the progress of the function. However, there is no value returned in R as

+the function creates three files that are used later by other EventPointer functions. 1) EventsFound.txt : Tab separated file with all

+the information of all the alternative splcing events found. 2) .flat file : Used to build the corresponding CDF file. 3) .CDF file: Output

+required for the aroma.affymetrix preprocessing pipeline. Both the .flat and .CDF file take large ammounts of memory in the hard drive, it is

+recommended to have at least 1.5 GB of free space.

+}

+\description{

+Generates the CDF file to be used under the aroma.affymetrix framework

+}

+\examples{

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

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

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

+   JunctionProbes<-paste(PathFiles,'/Junction_Probes.txt',sep='')

+   Directory<-tempdir()

+   microarray<-"HTA-2_0"

+

+  # Run the function

+

+   CDFfromGTF_Multipath(input='GTF',inputFile=DONSON_GTF,PSR=PSRProbes,Junc=JunctionProbes,PathCDF=Directory,microarray=microarray,paths=3)

+

+}