#### bugs in examples

JFerrer-B authored on 09/05/2022 07:38:25
Showing1 changed files
 ... ... @@ -44,6 +44,7 @@ recommended to have at least 1.5 GB of free space. 44 44  Generates the CDF file to be used under the aroma.affymetrix framework. 45 45  } 46 46  \examples{ 47 + \dontrun{ 47 48  PathFiles<-system.file('extdata',package='EventPointer') 48 49  DONSON_GTF<-paste(PathFiles,'/DONSON.gtf',sep='') 49 50  PSRProbes<-paste(PathFiles,'/PSR_Probes.txt',sep='') ... ... @@ -55,5 +56,6 @@ Generates the CDF file to be used under the aroma.affymetrix framework. 55 56   56 57  CDFfromGTF_Multipath(input='AffyGTF',inputFile=DONSON_GTF,PSR=PSRProbes,Junc=JunctionProbes, 57 58  PathCDF=Directory,microarray=microarray,paths=3) 59 + } 58 60   59 61  }

#### 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} 5 5  \title{CDF file creation for EventPointer (MultiPath)} 6 6  \usage{ 7 -CDFfromGTF_Multipath(input = "Ensembl", inputFile = NULL, PSR, Junc, 8 - PathCDF, microarray = NULL, paths = 2) 7 +CDFfromGTF_Multipath( 8 + input = "Ensembl", 9 + inputFile = NULL, 10 + PSR, 11 + Junc, 12 + PathCDF, 13 + microarray = NULL, 14 + paths = 2 15 +) 9 16  } 10 17  \arguments{ 11 18  \item{input}{Reference transcriptome used to build the CDF file. Must be one of Ensembl,

#### primers design option

Ferrer-Bonsoms Hernandez authored on 25/02/2019 08:58:27
Showing1 changed files
 ... ... @@ -2,7 +2,7 @@ 2 2  % Please edit documentation in R/CDFfromGTF_Multipath.R 3 3  \name{CDFfromGTF_Multipath} 4 4  \alias{CDFfromGTF_Multipath} 5 -\title{CDF file creation for EventPointer} 5 +\title{CDF file creation for EventPointer (MultiPath)} 6 6  \usage{ 7 7  CDFfromGTF_Multipath(input = "Ensembl", inputFile = NULL, PSR, Junc, 8 8  PathCDF, microarray = NULL, paths = 2) ... ... @@ -26,7 +26,7 @@ ClariomD, RTA or MTA} 26 26  } 27 27  \value{ 28 28  The function displays a progress bar to show the user the progress of the function. 29 -However, there is no value returned in R as the function creates three files that are used  29 +However, there is no value returned in R as the function creates three files that are used 30 30  later by other EventPointer functions. 1) EventsFound.txt : Tab separated file with all 31 31  the information of all the alternative splcing events found. 2) .flat file : Used to build 32 32  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 34 34  recommended to have at least 1.5 GB of free space. 35 35  } 36 36  \description{ 37 -Generates the CDF file to be used under the aroma.affymetrix framework 37 +Generates the CDF file to be used under the aroma.affymetrix framework. 38 38  } 39 39  \examples{ 40 40  PathFiles<-system.file('extdata',package='EventPointer')

#### JAF: cambios con formatR

Ferrer-Bonsoms Hernandez authored on 19/10/2018 11:41:13
Showing1 changed files
 ... ... @@ -42,7 +42,7 @@ Generates the CDF file to be used under the aroma.affymetrix framework 42 42  PSRProbes<-paste(PathFiles,'/PSR_Probes.txt',sep='') 43 43  JunctionProbes<-paste(PathFiles,'/Junction_Probes.txt',sep='') 44 44  Directory<-tempdir() 45 - microarray<-"HTA-2_0" 45 + microarray<-'HTA-2_0' 46 46   47 47  # Run the function 48 48 

#### JAF: correcciones 2

Ferrer-Bonsoms Hernandez authored on 16/10/2018 12:39:31
Showing1 changed files
 ... ... @@ -8,7 +8,8 @@ CDFfromGTF_Multipath(input = "Ensembl", inputFile = NULL, PSR, Junc, 8 8  PathCDF, microarray = NULL, paths = 2) 9 9  } 10 10  \arguments{ 11 -\item{input}{Reference transcriptome used to build the CDF file. Must be one of Ensembl, UCSC or GTF.} 11 +\item{input}{Reference transcriptome used to build the CDF file. Must be one of Ensembl, 12 +UCSC or GTF.} 12 13   13 14  \item{inputFile}{If input is GTF, inputFile should point to the GTF file to be used.} 14 15   ... ... @@ -18,15 +19,18 @@ CDFfromGTF_Multipath(input = "Ensembl", inputFile = NULL, PSR, Junc, 18 19   19 20  \item{PathCDF}{Directory where the output will be saved} 20 21   21 -\item{microarray}{Microarray used to create the CDF file. Must be one of: HTA-2_0, ClariomD, RTA or MTA} 22 +\item{microarray}{Microarray used to create the CDF file. Must be one of: HTA-2_0, 23 +ClariomD, RTA or MTA} 22 24   23 25  \item{paths}{Maximum number of paths of the events to find.} 24 26  } 25 27  \value{ 26 -The function displays a progress bar to show the user the progress of the function. However, there is no value returned in R as 27 -the function creates three files that are used later by other EventPointer functions. 1) EventsFound.txt : Tab separated file with all 28 -the information of all the alternative splcing events found. 2) .flat file : Used to build the corresponding CDF file. 3) .CDF file: Output 29 -required for the aroma.affymetrix preprocessing pipeline. Both the .flat and .CDF file take large ammounts of memory in the hard drive, it is 28 +The function displays a progress bar to show the user the progress of the function. 29 +However, there is no value returned in R as the function creates three files that are used  30 +later by other EventPointer functions. 1) EventsFound.txt : Tab separated file with all 31 +the information of all the alternative splcing events found. 2) .flat file : Used to build 32 +the corresponding CDF file. 3) .CDF file: Output required for the aroma.affymetrix preprocessing 33 +pipeline. Both the .flat and .CDF file take large ammounts of memory in the hard drive, it is 30 34  recommended to have at least 1.5 GB of free space. 31 35  } 32 36  \description{ ... ... @@ -42,6 +46,7 @@ Generates the CDF file to be used under the aroma.affymetrix framework 42 46   43 47  # Run the function 44 48   45 - CDFfromGTF_Multipath(input='AffyGTF',inputFile=DONSON_GTF,PSR=PSRProbes,Junc=JunctionProbes,PathCDF=Directory,microarray=microarray,paths=3) 49 + CDFfromGTF_Multipath(input='AffyGTF',inputFile=DONSON_GTF,PSR=PSRProbes,Junc=JunctionProbes, 50 + PathCDF=Directory,microarray=microarray,paths=3) 46 51   47 52  }

#### JAF: correccines 16/10/2018

Ferrer-Bonsoms Hernandez authored on 16/10/2018 09:03:42
Showing1 changed files
 ... ... @@ -42,6 +42,6 @@ Generates the CDF file to be used under the aroma.affymetrix framework 42 42   43 43  # Run the function 44 44   45 - CDFfromGTF_Multipath(input='GTF',inputFile=DONSON_GTF,PSR=PSRProbes,Junc=JunctionProbes,PathCDF=Directory,microarray=microarray,paths=3) 45 + CDFfromGTF_Multipath(input='AffyGTF',inputFile=DONSON_GTF,PSR=PSRProbes,Junc=JunctionProbes,PathCDF=Directory,microarray=microarray,paths=3) 46 46   47 47  }

#### JAF:cambios biocchek y chek de R

Ferrer-Bonsoms Hernandez authored on 04/10/2018 10:34:25
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 1 1 new file mode 100644 ... ... @@ -0,0 +1,47 @@ 1 +% Generated by roxygen2: do not edit by hand 2 +% Please edit documentation in R/CDFfromGTF_Multipath.R 3 +\name{CDFfromGTF_Multipath} 4 +\alias{CDFfromGTF_Multipath} 5 +\title{CDF file creation for EventPointer} 6 +\usage{ 7 +CDFfromGTF_Multipath(input = "Ensembl", inputFile = NULL, PSR, Junc, 8 + PathCDF, microarray = NULL, paths = 2) 9 +} 10 +\arguments{ 11 +\item{input}{Reference transcriptome used to build the CDF file. Must be one of Ensembl, UCSC or GTF.} 12 + 13 +\item{inputFile}{If input is GTF, inputFile should point to the GTF file to be used.} 14 + 15 +\item{PSR}{Path to the Exon probes txt file} 16 + 17 +\item{Junc}{Path to the Junction probes txt file} 18 + 19 +\item{PathCDF}{Directory where the output will be saved} 20 + 21 +\item{microarray}{Microarray used to create the CDF file. Must be one of: HTA-2_0, ClariomD, RTA or MTA} 22 + 23 +\item{paths}{Maximum number of paths of the events to find.} 24 +} 25 +\value{ 26 +The function displays a progress bar to show the user the progress of the function. However, there is no value returned in R as 27 +the function creates three files that are used later by other EventPointer functions. 1) EventsFound.txt : Tab separated file with all 28 +the information of all the alternative splcing events found. 2) .flat file : Used to build the corresponding CDF file. 3) .CDF file: Output 29 +required for the aroma.affymetrix preprocessing pipeline. Both the .flat and .CDF file take large ammounts of memory in the hard drive, it is 30 +recommended to have at least 1.5 GB of free space. 31 +} 32 +\description{ 33 +Generates the CDF file to be used under the aroma.affymetrix framework 34 +} 35 +\examples{ 36 + PathFiles<-system.file('extdata',package='EventPointer') 37 + DONSON_GTF<-paste(PathFiles,'/DONSON.gtf',sep='') 38 + PSRProbes<-paste(PathFiles,'/PSR_Probes.txt',sep='') 39 + JunctionProbes<-paste(PathFiles,'/Junction_Probes.txt',sep='') 40 + Directory<-tempdir() 41 + microarray<-"HTA-2_0" 42 + 43 + # Run the function 44 + 45 + CDFfromGTF_Multipath(input='GTF',inputFile=DONSON_GTF,PSR=PSRProbes,Junc=JunctionProbes,PathCDF=Directory,microarray=microarray,paths=3) 46 + 47 +}