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bugs in examples

JFerrer-B authored on 09/05/2022 07:38:25
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@@ -44,6 +44,7 @@ recommended to have at least 1.5 GB of free space.
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 Generates the CDF file to be used under the aroma.affymetrix framework.
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 }
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 \examples{
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+ \dontrun{
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    PathFiles<-system.file('extdata',package='EventPointer')
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    DONSON_GTF<-paste(PathFiles,'/DONSON.gtf',sep='')
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    PSRProbes<-paste(PathFiles,'/PSR_Probes.txt',sep='')
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@@ -55,5 +56,6 @@ Generates the CDF file to be used under the aroma.affymetrix framework.
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    CDFfromGTF_Multipath(input='AffyGTF',inputFile=DONSON_GTF,PSR=PSRProbes,Junc=JunctionProbes,
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                         PathCDF=Directory,microarray=microarray,paths=3)
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+ }
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 }
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jaf_ update to EventPointer 3.0

Juan Angel Ferrer B authored on 21/12/2020 16:47:26
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@@ -4,8 +4,15 @@
4 4
 \alias{CDFfromGTF_Multipath}
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 \title{CDF file creation for EventPointer (MultiPath)}
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 \usage{
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-CDFfromGTF_Multipath(input = "Ensembl", inputFile = NULL, PSR, Junc,
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-  PathCDF, microarray = NULL, paths = 2)
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+CDFfromGTF_Multipath(
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+  input = "Ensembl",
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+  inputFile = NULL,
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+  PSR,
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+  Junc,
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+  PathCDF,
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+  microarray = NULL,
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+  paths = 2
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+)
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 }
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 \arguments{
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 \item{input}{Reference transcriptome used to build the CDF file. Must be one of Ensembl,
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primers design option

Ferrer-Bonsoms Hernandez authored on 25/02/2019 08:58:27
Showing1 changed files
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@@ -2,7 +2,7 @@
2 2
 % Please edit documentation in R/CDFfromGTF_Multipath.R
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 \name{CDFfromGTF_Multipath}
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 \alias{CDFfromGTF_Multipath}
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-\title{CDF file creation for EventPointer}
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+\title{CDF file creation for EventPointer (MultiPath)}
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 \usage{
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 CDFfromGTF_Multipath(input = "Ensembl", inputFile = NULL, PSR, Junc,
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   PathCDF, microarray = NULL, paths = 2)
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@@ -26,7 +26,7 @@ ClariomD, RTA or MTA}
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 }
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 \value{
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 The function displays a progress bar to show the user the progress of the function.
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-However, there is no value returned in R as the function creates three files that are used 
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+However, there is no value returned in R as the function creates three files that are used
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 later by other EventPointer functions. 1) EventsFound.txt : Tab separated file with all
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 the information of all the alternative splcing events found. 2) .flat file : Used to build
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 the corresponding CDF file. 3) .CDF file: Output required for the aroma.affymetrix preprocessing
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@@ -34,7 +34,7 @@ pipeline. Both the .flat and .CDF file take large ammounts of memory in the hard
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 recommended to have at least 1.5 GB of free space.
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 }
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 \description{
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-Generates the CDF file to be used under the aroma.affymetrix framework
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+Generates the CDF file to be used under the aroma.affymetrix framework.
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 }
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 \examples{
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    PathFiles<-system.file('extdata',package='EventPointer')
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JAF: cambios con formatR

Ferrer-Bonsoms Hernandez authored on 19/10/2018 11:41:13
Showing1 changed files
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@@ -42,7 +42,7 @@ Generates the CDF file to be used under the aroma.affymetrix framework
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    PSRProbes<-paste(PathFiles,'/PSR_Probes.txt',sep='')
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    JunctionProbes<-paste(PathFiles,'/Junction_Probes.txt',sep='')
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    Directory<-tempdir()
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-   microarray<-"HTA-2_0"
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+   microarray<-'HTA-2_0'
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   # Run the function
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JAF: correcciones 2

Ferrer-Bonsoms Hernandez authored on 16/10/2018 12:39:31
Showing1 changed files
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@@ -8,7 +8,8 @@ CDFfromGTF_Multipath(input = "Ensembl", inputFile = NULL, PSR, Junc,
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   PathCDF, microarray = NULL, paths = 2)
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 }
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 \arguments{
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-\item{input}{Reference transcriptome used to build the CDF file. Must be one of Ensembl, UCSC or GTF.}
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+\item{input}{Reference transcriptome used to build the CDF file. Must be one of Ensembl,
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+UCSC or GTF.}
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 \item{inputFile}{If input is GTF, inputFile should point to the GTF file to be used.}
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... ...
@@ -18,15 +19,18 @@ CDFfromGTF_Multipath(input = "Ensembl", inputFile = NULL, PSR, Junc,
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 \item{PathCDF}{Directory where the output will be saved}
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-\item{microarray}{Microarray used to create the CDF file. Must be one of: HTA-2_0, ClariomD, RTA or MTA}
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+\item{microarray}{Microarray used to create the CDF file. Must be one of: HTA-2_0,
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+ClariomD, RTA or MTA}
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 \item{paths}{Maximum number of paths of the events to find.}
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 }
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 \value{
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-The function displays a progress bar to show the user the progress of the function. However, there is no value returned in R as
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-the function creates three files that are used later by other EventPointer functions. 1) EventsFound.txt : Tab separated file with all
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-the information of all the alternative splcing events found. 2) .flat file : Used to build the corresponding CDF file. 3) .CDF file: Output
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-required for the aroma.affymetrix preprocessing pipeline. Both the .flat and .CDF file take large ammounts of memory in the hard drive, it is
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+The function displays a progress bar to show the user the progress of the function.
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+However, there is no value returned in R as the function creates three files that are used 
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+later by other EventPointer functions. 1) EventsFound.txt : Tab separated file with all
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+the information of all the alternative splcing events found. 2) .flat file : Used to build
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+the corresponding CDF file. 3) .CDF file: Output required for the aroma.affymetrix preprocessing
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+pipeline. Both the .flat and .CDF file take large ammounts of memory in the hard drive, it is
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 recommended to have at least 1.5 GB of free space.
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 }
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 \description{
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@@ -42,6 +46,7 @@ Generates the CDF file to be used under the aroma.affymetrix framework
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   # Run the function
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-   CDFfromGTF_Multipath(input='AffyGTF',inputFile=DONSON_GTF,PSR=PSRProbes,Junc=JunctionProbes,PathCDF=Directory,microarray=microarray,paths=3)
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+   CDFfromGTF_Multipath(input='AffyGTF',inputFile=DONSON_GTF,PSR=PSRProbes,Junc=JunctionProbes,
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+                        PathCDF=Directory,microarray=microarray,paths=3)
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 }
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JAF: correccines 16/10/2018

Ferrer-Bonsoms Hernandez authored on 16/10/2018 09:03:42
Showing1 changed files
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@@ -42,6 +42,6 @@ Generates the CDF file to be used under the aroma.affymetrix framework
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   # Run the function
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-   CDFfromGTF_Multipath(input='GTF',inputFile=DONSON_GTF,PSR=PSRProbes,Junc=JunctionProbes,PathCDF=Directory,microarray=microarray,paths=3)
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+   CDFfromGTF_Multipath(input='AffyGTF',inputFile=DONSON_GTF,PSR=PSRProbes,Junc=JunctionProbes,PathCDF=Directory,microarray=microarray,paths=3)
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 }
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JAF:cambios biocchek y chek de R

Ferrer-Bonsoms Hernandez authored on 04/10/2018 10:34:25
Showing1 changed files
1 1
new file mode 100644
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@@ -0,0 +1,47 @@
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/CDFfromGTF_Multipath.R
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+\name{CDFfromGTF_Multipath}
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+\alias{CDFfromGTF_Multipath}
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+\title{CDF file creation for EventPointer}
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+\usage{
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+CDFfromGTF_Multipath(input = "Ensembl", inputFile = NULL, PSR, Junc,
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+  PathCDF, microarray = NULL, paths = 2)
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+}
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+\arguments{
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+\item{input}{Reference transcriptome used to build the CDF file. Must be one of Ensembl, UCSC or GTF.}
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+
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+\item{inputFile}{If input is GTF, inputFile should point to the GTF file to be used.}
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+
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+\item{PSR}{Path to the Exon probes txt file}
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+
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+\item{Junc}{Path to the Junction probes txt file}
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+
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+\item{PathCDF}{Directory where the output will be saved}
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+
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+\item{microarray}{Microarray used to create the CDF file. Must be one of: HTA-2_0, ClariomD, RTA or MTA}
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+
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+\item{paths}{Maximum number of paths of the events to find.}
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+}
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+\value{
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+The function displays a progress bar to show the user the progress of the function. However, there is no value returned in R as
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+the function creates three files that are used later by other EventPointer functions. 1) EventsFound.txt : Tab separated file with all
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+the information of all the alternative splcing events found. 2) .flat file : Used to build the corresponding CDF file. 3) .CDF file: Output
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+required for the aroma.affymetrix preprocessing pipeline. Both the .flat and .CDF file take large ammounts of memory in the hard drive, it is
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+recommended to have at least 1.5 GB of free space.
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+}
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+\description{
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+Generates the CDF file to be used under the aroma.affymetrix framework
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+}
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+\examples{
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+   PathFiles<-system.file('extdata',package='EventPointer')
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+   DONSON_GTF<-paste(PathFiles,'/DONSON.gtf',sep='')
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+   PSRProbes<-paste(PathFiles,'/PSR_Probes.txt',sep='')
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+   JunctionProbes<-paste(PathFiles,'/Junction_Probes.txt',sep='')
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+   Directory<-tempdir()
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+   microarray<-"HTA-2_0"
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+
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+  # Run the function
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+
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+   CDFfromGTF_Multipath(input='GTF',inputFile=DONSON_GTF,PSR=PSRProbes,Junc=JunctionProbes,PathCDF=Directory,microarray=microarray,paths=3)
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+
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+}