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@@ -2,7 +2,7 @@ Package: EventPointer |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: An effective identification of alternative splicing events |
| 4 | 4 |
using junction arrays and RNA-Seq data |
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-Version: 2.3.3 |
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+Version: 2.3.4 |
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| 6 | 6 |
Author: Juan Pablo Romero, Juan A. Ferrer-Bonsoms, Pablo Sacristan, Ander Muniategui, Fernando Carazo, Ander Aramburu, Angel Rubio |
| 7 | 7 |
Maintainer: Juan Pablo Romero <jpromero@ceit.es> |
| 8 | 8 |
Description: EventPointer is an R package to identify alternative splicing events |
| 10 | 10 |
deleted file mode 100644 |
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@@ -1,163 +0,0 @@ |
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-test_FindPrimers <- function() {
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- |
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- obs <- tryCatch(FindPrimers(SG = NULL, |
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- EventNum = 4, |
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- Primer3Path = "C:\\PROGRA~2\\primer3\\PRIMER~1.EXE", |
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- Dir = "C:\\PROGRA~2\\primer3\\", |
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- taqman = 1, |
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- nProbes=1, |
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- nPrimerstwo=4, |
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- ncommonForward=4, |
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- ncommonReverse=4, |
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- nExons=10, |
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- nPrimers =5, |
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- maxLength = 1200), error=conditionMessage) |
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- |
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- checkIdentical("SG field is empty", obs)
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- |
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- obs <- tryCatch( |
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- FindPrimers(SG = list(), |
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- EventNum = 0, |
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- Primer3Path = "C:\\PROGRA~2\\primer3\\PRIMER~1.EXE", |
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- Dir = "C:\\PROGRA~2\\primer3\\", |
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- taqman = 1, |
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- nProbes=1, |
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- nPrimerstwo=4, |
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- ncommonForward=4, |
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- ncommonReverse=4, |
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- nExons=10, |
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- nPrimers =5, |
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- maxLength = 1200), error=conditionMessage) |
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- checkIdentical("EventNum field is empty or is not > 0", obs)
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- |
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- obs <- tryCatch( |
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- FindPrimers(SG = list(), |
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- EventNum = -45, |
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- Primer3Path = "C:\\PROGRA~2\\primer3\\PRIMER~1.EXE", |
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- Dir = "C:\\PROGRA~2\\primer3\\", |
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- taqman = 1, |
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- nProbes=1, |
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- nPrimerstwo=4, |
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- ncommonForward=4, |
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- ncommonReverse=4, |
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- nExons=10, |
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- nPrimers =5, |
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- maxLength = 1200), error=conditionMessage) |
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- checkIdentical("EventNum field is empty or is not > 0", obs)
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- |
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- obs <- tryCatch( |
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- FindPrimers(SG = list(), |
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- EventNum = NULL, |
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- Primer3Path = "C:\\PROGRA~2\\primer3\\PRIMER~1.EXE", |
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- Dir = "C:\\PROGRA~2\\primer3\\", |
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- taqman = 1, |
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- nProbes=1, |
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- nPrimerstwo=4, |
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- ncommonForward=4, |
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- ncommonReverse=4, |
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- nExons=10, |
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- nPrimers =5, |
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- maxLength = 1200), error=conditionMessage) |
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- checkIdentical("EventNum field is empty or is not > 0", obs)
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- |
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- |
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- obs <- tryCatch( |
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- FindPrimers(SG = list(), |
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- EventNum = 4, |
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- Primer3Path = "", |
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- Dir = "C:\\PROGRA~2\\primer3\\", |
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- taqman = 1, |
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- nProbes=1, |
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- nPrimerstwo=4, |
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- ncommonForward=4, |
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- ncommonReverse=4, |
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- nExons=10, |
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- nPrimers =5, |
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- maxLength = 1200), error=conditionMessage) |
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- checkIdentical("Primer3Path field should point to the .exe of Primers3.
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- Check in the vignette for more information", obs) |
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- |
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- obs <- tryCatch( |
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- FindPrimers(SG = list(), |
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- EventNum = 4, |
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- Primer3Path = NULL, |
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- Dir = "C:\\PROGRA~2\\primer3\\", |
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- taqman = 1, |
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- nProbes=1, |
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- nPrimerstwo=4, |
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- ncommonForward=4, |
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- ncommonReverse=4, |
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- nExons=10, |
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- nPrimers =5, |
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- maxLength = 1200), error=conditionMessage) |
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- checkIdentical("Primer3Path field is empty", obs)
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- |
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- |
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- |
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- |
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- |
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- # obs <- tryCatch( |
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- # FindPrimers(SG = list(), |
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- # EventNum = 1, |
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- # Primer3Path = "./inst/extdata/DONSON.gtf", |
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- # Dir = "", |
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- # taqman = 1, |
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- # nProbes=1, |
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- # nPrimerstwo=4, |
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- # ncommonForward=4, |
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- # ncommonReverse=4, |
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- # nExons=10, |
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- # nPrimers =5, |
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- # maxLength = 1200), error=conditionMessage) |
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- # checkIdentical("Dir = Complete path where primer3web_v4_0_0_default_settings.txt file and primer3_config directory are stored", obs)
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- # |
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- |
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- |
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- obs <- tryCatch( |
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- FindPrimers(SG = list(), |
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- EventNum = 1, |
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- Primer3Path = "./inst/extdata/DONSON.gtf", |
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- Dir = NULL, |
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- taqman = 1, |
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- nProbes=1, |
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- nPrimerstwo=4, |
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- ncommonForward=4, |
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- ncommonReverse=4, |
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- nExons=10, |
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- nPrimers =5, |
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- maxLength = 1200), error=conditionMessage) |
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- checkIdentical("Dir field is empty", obs)
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- |
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- obs <- tryCatch( |
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- FindPrimers(SG = list(), |
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- EventNum = 1, |
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- Primer3Path = "./inst/extdata/DONSON.gtf", |
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- Dir = "C:\\PROGRA~2\\primer3\\", |
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- taqman = NA, |
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- nProbes=1, |
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- nPrimerstwo=4, |
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- ncommonForward=4, |
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- ncommonReverse=4, |
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- nExons=10, |
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- nPrimers =5, |
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- maxLength = 1200), error=conditionMessage) |
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- checkIdentical("taqman field is empty", obs)
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- |
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- |
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- obs <- tryCatch( |
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- FindPrimers(SG = list(), |
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- EventNum = 1, |
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- Primer3Path = "C:\\PROGRA~2\\primer3\\PRIMER~1.EXE", |
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- Dir = "C:\\PROGRA~2\\primer3\\", |
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- taqman = 3, |
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- nProbes=1, |
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- nPrimerstwo=4, |
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- ncommonForward=4, |
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- ncommonReverse=4, |
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- nExons=10, |
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- nPrimers =5, |
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- maxLength = 1200), error=conditionMessage) |
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- checkIdentical("taqman variable should be equal to 1 or 0", obs)
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- |
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- |
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-} |
