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Commit d03a0ecc authored by VladaMilch's avatar VladaMilch
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Package name changed from pdProbeRemap

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DESCRIPTION
View file @ d03a0ecc
Package: pdProbeRemap
Package: arrayProbeRemap
Type: Package
Title: What the package does (short line)
Version: 0.0.0
......
R/1_SAM_read.R
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......@@ -9,7 +9,7 @@
#' @author Grischa Toedt, Vladislava Milchevskaya \email{milchv@gmail.com}
#' @examples
#' sam_file <-
#' dir(system.file("extdata",package="pdProbeRemap"),
#' dir(system.file("extdata",package="arrayProbeRemap"),
#' pattern="example_drosophila.Aligned.out.sam",
#' full.names=TRUE)
#' SAM_list <- read.sam(sam_file)
......
R/2_processAlignments.R
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......@@ -13,7 +13,7 @@
#' @author Vladislava Milchevskaya \email{milchv@gmail.com}
#' @examples
#' sam_file <-
#' dir(system.file("extdata",package="pdProbeRemap"),
#' dir(system.file("extdata",package="arrayProbeRemap"),
#' pattern="example_drosophila.Aligned.out.sam",full.names=TRUE)
#' alignment_dir <-
#' strsplit(sam_file, split = "example_drosophila.Aligned.out.sam")[[1]]
......
R/94_makeNewAnnotationPackage.R
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......@@ -19,11 +19,11 @@
#' data("Annotation_example")
#' data("seed_example")
#' alignmentDir <-
#' unlist(strsplit(dir(system.file("extdata",package="pdProbeRemap"),
#' unlist(strsplit(dir(system.file("extdata",package="arrayProbeRemap"),
#' pattern="example_drosophila.Aligned.out.sam",
#' full.names=TRUE), split = "example_drosophila.Aligned.out.sam"))[1]
#'
#' outputDir_example = system.file("data", package = "pdProbeRemap")
#' outputDir_example = system.file("data", package = "arrayProbeRemap")
#'
#' \dontrun{
#' makeNewAnnotationPackage(alignment.dir = alignmentDir,
......@@ -95,4 +95,4 @@ makeNewAnnotationPackage_inner <- function(alignment.dir,
annotation_type = package_seed[[3]])
return(NEW_ParsedData)
}
\ No newline at end of file
}
inst/doc/pdProbeRemap.R → inst/doc/arrayProbeRemap.R
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## ---- message=FALSE------------------------------------------------------
library("pdProbeRemap")
library("arrayProbeRemap")
## ---- eval = FALSE-------------------------------------------------------
# #evaluation worked
......@@ -59,12 +59,12 @@ library("pdProbeRemap")
# # package_seed)
#
#
# library("pdProbeRemap")
# data(Alignments_class_example, package = "pdProbeRemap")
# library("arrayProbeRemap")
# data(Alignments_class_example, package = "arrayProbeRemap")
# data(Annotation_example)
# data(seed_example)
# alignmentDir <-
# unlist(strsplit(dir(system.file("extdata",package="pdProbeRemap"),
# unlist(strsplit(dir(system.file("extdata",package="arrayProbeRemap"),
# pattern="example_drosophila.Aligned.out.sam",
# full.names=TRUE), split = "example_drosophila.Aligned.out.sam"))[1]
#
......@@ -79,7 +79,7 @@ library("pdProbeRemap")
#
## ---- eval = FALSE-------------------------------------------------------
# library("pdProbeRemap")
# library("arrayProbeRemap")
#
# alignmentDir = "/Users/milchevs/Documents/Biology/PROJECTS/Paul_Bertone/ReANNot/MoGene2/"
# load("/Users/milchevs/Documents/Biology/PROJECTS/Paul_Bertone/ReANNot/Annotations/AnnotationDataFrame.Mus_musculus.GRCm38.82.RData")
......@@ -88,7 +88,7 @@ library("pdProbeRemap")
#
## ---- eval = FALSE-------------------------------------------------------
# o1 = pdProbeRemap::makeOriginalPackageObject(originalAnnotationDir = dir1,
# o1 = arrayProbeRemap::makeOriginalPackageObject(originalAnnotationDir = dir1,
# organism = "Mouse",
# species = "Mus musculus",
# outputDir = outDir )
......@@ -119,7 +119,7 @@ library("pdProbeRemap")
# pkgname = "pd.NEWPACKAGE")
## ---- eval = FALSE-------------------------------------------------------
# library("pdProbeRemap")
# library("arrayProbeRemap")
#
# outDir <- "/Users/milchevs/ownCloud/ProbeRemapStep3/R/testdata/DroGene1_1"
# OriginalAnnotDir <- "/Users/milchevs/Downloads/CD_DrosGenome1\ 2/Full/DrosGenome1/LibFiles/"
......
inst/doc/pdProbeRemap.Rmd → inst/doc/arrayProbeRemap.Rmd
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---
title: "pdProbeRemap"
title: "arrayProbeRemap"
output: rmarkdown::pdf_document
vignette: >
%\VignetteIndexEntry{Put the title of your vignette here}
......@@ -50,7 +50,7 @@ For that reason annotation building procedure is split in three steps:
## Load the package
```{r, message=FALSE}
library("pdProbeRemap")
library("arrayProbeRemap")
```
## Set up an aligner
......@@ -151,12 +151,12 @@ o1 = makeOriginalPackageObject(originalAnnotationDir = dir1,
# package_seed)
library("pdProbeRemap")
data(Alignments_class_example, package = "pdProbeRemap")
library("arrayProbeRemap")
data(Alignments_class_example, package = "arrayProbeRemap")
data(Annotation_example)
data(seed_example)
alignmentDir <-
unlist(strsplit(dir(system.file("extdata",package="pdProbeRemap"),
unlist(strsplit(dir(system.file("extdata",package="arrayProbeRemap"),
pattern="example_drosophila.Aligned.out.sam",
full.names=TRUE), split = "example_drosophila.Aligned.out.sam"))[1]
......@@ -175,7 +175,7 @@ makeNewAnnotationPackage(alignment.dir = alignmentDir,
## generation of the new annotation data for PGF-based affy annotations
```{r, eval = FALSE}
library("pdProbeRemap")
library("arrayProbeRemap")
alignmentDir = "/Users/milchevs/Documents/Biology/PROJECTS/Paul_Bertone/ReANNot/MoGene2/"
load("/Users/milchevs/Documents/Biology/PROJECTS/Paul_Bertone/ReANNot/Annotations/AnnotationDataFrame.Mus_musculus.GRCm38.82.RData")
......@@ -185,7 +185,7 @@ outDir = "/Users/milchevs/ownCloud/ProbeRemapSteps14/OutPutDir/Probe_Sequences_F
```
```{r, eval = FALSE}
o1 = pdProbeRemap::makeOriginalPackageObject(originalAnnotationDir = dir1,
o1 = arrayProbeRemap::makeOriginalPackageObject(originalAnnotationDir = dir1,
organism = "Mouse",
species = "Mus musculus",
outputDir = outDir )
......@@ -232,7 +232,7 @@ celfiles = read.celfiles(filenames=CelFilesPath,
# One complete example of new annotation package building
```{r, eval = FALSE}
library("pdProbeRemap")
library("arrayProbeRemap")
outDir <- "/Users/milchevs/ownCloud/ProbeRemapStep3/R/testdata/DroGene1_1"
OriginalAnnotDir <- "/Users/milchevs/Downloads/CD_DrosGenome1\ 2/Full/DrosGenome1/LibFiles/"
......
man/filter.T.alignment.Rd
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......@@ -4,7 +4,7 @@
\alias{filter.T.alignment}
\title{filter out non-unique transcriptomic mappings}
\usage{
filter.T.alignment(AT, level)
\method{filter}{T.alignment}(AT, level)
}
\arguments{
\item{AT}{annoated transcriptomic alignment, \code{"data.frame"}}
......
man/makeNewAnnotationPackage.Rd
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......@@ -38,11 +38,11 @@ data("Alignments_class_example")
data("Annotation_example")
data("seed_example")
alignmentDir <-
unlist(strsplit(dir(system.file("extdata",package="pdProbeRemap"),
unlist(strsplit(dir(system.file("extdata",package="arrayProbeRemap"),
pattern="example_drosophila.Aligned.out.sam",
full.names=TRUE), split = "example_drosophila.Aligned.out.sam"))[1]
outputDir_example = system.file("data", package = "pdProbeRemap")
outputDir_example = system.file("data", package = "arrayProbeRemap")
\dontrun{
makeNewAnnotationPackage(alignment.dir = alignmentDir,
......
man/processAlignments.Rd
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......@@ -25,7 +25,7 @@ and generated an object of class \code{"Alignments"}
}
\examples{
sam_file <-
dir(system.file("extdata",package="pdProbeRemap"),
dir(system.file("extdata",package="arrayProbeRemap"),
pattern="example_drosophila.Aligned.out.sam",full.names=TRUE)
alignment_dir <-
strsplit(sam_file, split = "example_drosophila.Aligned.out.sam")[[1]]
......
man/read.sam.Rd
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......@@ -21,7 +21,7 @@ a \code{"data.frame"}.
}
\examples{
sam_file <-
dir(system.file("extdata",package="pdProbeRemap"),
dir(system.file("extdata",package="arrayProbeRemap"),
pattern="example_drosophila.Aligned.out.sam",
full.names=TRUE)
SAM_list <- read.sam(sam_file)
......
tests/testthat.R
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library("testthat")
library("pdProbeRemap")
library("arrayProbeRemap")
test_check("pdProbeRemap")
test_check("arrayProbeRemap")
tests/testthat/test_91.R
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......@@ -38,8 +38,8 @@
# library(devtools)
# library(roxygen2)
# library(testthat)
# library("pdProbeRemap")
# load_all("pdProbeRemap")
# library("arrayProbeRemap")
# load_all("arrayProbeRemap")
#
# PDnew <- build_new_ParsedDataOld_object_PGF(level = level, ParsedDataOld = ParsedData, PS_controls = PS_controls, Annotation = Annotation, ProbeSetData = PSD)
# debug(build_new_ParsedDataOld_object_PGF)
......
vignettes/pdProbeRemap.Rmd → vignettes/arrayProbeRemap.Rmd
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---
title: "pdProbeRemap"
title: "arrayProbeRemap"
output: rmarkdown::pdf_document
vignette: >
%\VignetteIndexEntry{Put the title of your vignette here}
......@@ -50,7 +50,7 @@ For that reason annotation building procedure is split in three steps:
## Load the package
```{r, message=FALSE}
library("pdProbeRemap")
library("arrayProbeRemap")
```
## Set up an aligner
......@@ -151,12 +151,12 @@ o1 = makeOriginalPackageObject(originalAnnotationDir = dir1,
# package_seed)
library("pdProbeRemap")
data(Alignments_class_example, package = "pdProbeRemap")
library("arrayProbeRemap")
data(Alignments_class_example, package = "arrayProbeRemap")
data(Annotation_example)
data(seed_example)
alignmentDir <-
unlist(strsplit(dir(system.file("extdata",package="pdProbeRemap"),
unlist(strsplit(dir(system.file("extdata",package="arrayProbeRemap"),
pattern="example_drosophila.Aligned.out.sam",
full.names=TRUE), split = "example_drosophila.Aligned.out.sam"))[1]
......@@ -175,7 +175,7 @@ makeNewAnnotationPackage(alignment.dir = alignmentDir,
## generation of the new annotation data for PGF-based affy annotations
```{r, eval = FALSE}
library("pdProbeRemap")
library("arrayProbeRemap")
alignmentDir = "/Users/milchevs/Documents/Biology/PROJECTS/Paul_Bertone/ReANNot/MoGene2/"
load("/Users/milchevs/Documents/Biology/PROJECTS/Paul_Bertone/ReANNot/Annotations/AnnotationDataFrame.Mus_musculus.GRCm38.82.RData")
......@@ -185,7 +185,7 @@ outDir = "/Users/milchevs/ownCloud/ProbeRemapSteps14/OutPutDir/Probe_Sequences_F
```
```{r, eval = FALSE}
o1 = pdProbeRemap::makeOriginalPackageObject(originalAnnotationDir = dir1,
o1 = arrayProbeRemap::makeOriginalPackageObject(originalAnnotationDir = dir1,
organism = "Mouse",
species = "Mus musculus",
outputDir = outDir )
......@@ -232,7 +232,7 @@ celfiles = read.celfiles(filenames=CelFilesPath,
# One complete example of new annotation package building
```{r, eval = FALSE}
library("pdProbeRemap")
library("arrayProbeRemap")
outDir <- "/Users/milchevs/ownCloud/ProbeRemapStep3/R/testdata/DroGene1_1"
OriginalAnnotDir <- "/Users/milchevs/Downloads/CD_DrosGenome1\ 2/Full/DrosGenome1/LibFiles/"
......
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