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Vladislava Milchevskaya
arrayProbeRemap
Commits
d03a0ecc
Commit
d03a0ecc
authored
Jan 10, 2018
by
VladaMilch
Browse files
Package name changed from pdProbeRemap
parent
2a476c9f
Changes
14
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DESCRIPTION
View file @
d03a0ecc
Package:
pd
ProbeRemap
Package:
array
ProbeRemap
Type: Package
Title: What the package does (short line)
Version: 0.0.0
...
...
R/1_SAM_read.R
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d03a0ecc
...
...
@@ -9,7 +9,7 @@
#' @author Grischa Toedt, Vladislava Milchevskaya \email{milchv@gmail.com}
#' @examples
#' sam_file <-
#' dir(system.file("extdata",package="
pd
ProbeRemap"),
#' dir(system.file("extdata",package="
array
ProbeRemap"),
#' 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="
pd
ProbeRemap"),
#' dir(system.file("extdata",package="
array
ProbeRemap"),
#' 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="
pd
ProbeRemap"),
#' unlist(strsplit(dir(system.file("extdata",package="
array
ProbeRemap"),
#' pattern="example_drosophila.Aligned.out.sam",
#' full.names=TRUE), split = "example_drosophila.Aligned.out.sam"))[1]
#'
#' outputDir_example = system.file("data", package = "
pd
ProbeRemap")
#' outputDir_example = system.file("data", package = "
array
ProbeRemap")
#'
#' \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/
pd
ProbeRemap.R
→
inst/doc/
array
ProbeRemap.R
View file @
d03a0ecc
## ---- message=FALSE------------------------------------------------------
library
(
"
pd
ProbeRemap"
)
library
(
"
array
ProbeRemap"
)
## ---- eval = FALSE-------------------------------------------------------
# #evaluation worked
...
...
@@ -59,12 +59,12 @@ library("pdProbeRemap")
# # package_seed)
#
#
# library("
pd
ProbeRemap")
# data(Alignments_class_example, package = "
pd
ProbeRemap")
# library("
array
ProbeRemap")
# data(Alignments_class_example, package = "
array
ProbeRemap")
# data(Annotation_example)
# data(seed_example)
# alignmentDir <-
# unlist(strsplit(dir(system.file("extdata",package="
pd
ProbeRemap"),
# unlist(strsplit(dir(system.file("extdata",package="
array
ProbeRemap"),
# 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("
pd
ProbeRemap")
# library("
array
ProbeRemap")
#
# 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 =
pd
ProbeRemap::makeOriginalPackageObject(originalAnnotationDir = dir1,
# o1 =
array
ProbeRemap::makeOriginalPackageObject(originalAnnotationDir = dir1,
# organism = "Mouse",
# species = "Mus musculus",
# outputDir = outDir )
...
...
@@ -119,7 +119,7 @@ library("pdProbeRemap")
# pkgname = "pd.NEWPACKAGE")
## ---- eval = FALSE-------------------------------------------------------
# library("
pd
ProbeRemap")
# library("
array
ProbeRemap")
#
# outDir <- "/Users/milchevs/ownCloud/ProbeRemapStep3/R/testdata/DroGene1_1"
# OriginalAnnotDir <- "/Users/milchevs/Downloads/CD_DrosGenome1\ 2/Full/DrosGenome1/LibFiles/"
...
...
inst/doc/
pd
ProbeRemap.Rmd
→
inst/doc/
array
ProbeRemap.Rmd
View file @
d03a0ecc
---
title: "
pd
ProbeRemap"
title: "
array
ProbeRemap"
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("
pd
ProbeRemap")
library("
array
ProbeRemap")
```
## Set up an aligner
...
...
@@ -151,12 +151,12 @@ o1 = makeOriginalPackageObject(originalAnnotationDir = dir1,
# package_seed)
library("
pd
ProbeRemap")
data(Alignments_class_example, package = "
pd
ProbeRemap")
library("
array
ProbeRemap")
data(Alignments_class_example, package = "
array
ProbeRemap")
data(Annotation_example)
data(seed_example)
alignmentDir <-
unlist(strsplit(dir(system.file("extdata",package="
pd
ProbeRemap"),
unlist(strsplit(dir(system.file("extdata",package="
array
ProbeRemap"),
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("
pd
ProbeRemap")
library("
array
ProbeRemap")
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 =
pd
ProbeRemap::makeOriginalPackageObject(originalAnnotationDir = dir1,
o1 =
array
ProbeRemap::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("
pd
ProbeRemap")
library("
array
ProbeRemap")
outDir <- "/Users/milchevs/ownCloud/ProbeRemapStep3/R/testdata/DroGene1_1"
OriginalAnnotDir <- "/Users/milchevs/Downloads/CD_DrosGenome1\ 2/Full/DrosGenome1/LibFiles/"
...
...
inst/doc/
pd
ProbeRemap.pdf
→
inst/doc/
array
ProbeRemap.pdf
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d03a0ecc
No preview for this file type
man/filter.T.alignment.Rd
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d03a0ecc
...
...
@@ -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="
pd
ProbeRemap"),
unlist(strsplit(dir(system.file("extdata",package="
array
ProbeRemap"),
pattern="example_drosophila.Aligned.out.sam",
full.names=TRUE), split = "example_drosophila.Aligned.out.sam"))[1]
outputDir_example = system.file("data", package = "
pd
ProbeRemap")
outputDir_example = system.file("data", package = "
array
ProbeRemap")
\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="
pd
ProbeRemap"),
dir(system.file("extdata",package="
array
ProbeRemap"),
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="
pd
ProbeRemap"),
dir(system.file("extdata",package="
array
ProbeRemap"),
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
(
"
pd
ProbeRemap"
)
library
(
"
array
ProbeRemap"
)
test_check
(
"
pd
ProbeRemap"
)
test_check
(
"
array
ProbeRemap"
)
tests/testthat/test_91.R
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d03a0ecc
...
...
@@ -38,8 +38,8 @@
# library(devtools)
# library(roxygen2)
# library(testthat)
# library("
pd
ProbeRemap")
# load_all("
pd
ProbeRemap")
# library("
array
ProbeRemap")
# load_all("
array
ProbeRemap")
#
# 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/
pd
ProbeRemap.Rmd
→
vignettes/
array
ProbeRemap.Rmd
View file @
d03a0ecc
---
title: "
pd
ProbeRemap"
title: "
array
ProbeRemap"
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("
pd
ProbeRemap")
library("
array
ProbeRemap")
```
## Set up an aligner
...
...
@@ -151,12 +151,12 @@ o1 = makeOriginalPackageObject(originalAnnotationDir = dir1,
# package_seed)
library("
pd
ProbeRemap")
data(Alignments_class_example, package = "
pd
ProbeRemap")
library("
array
ProbeRemap")
data(Alignments_class_example, package = "
array
ProbeRemap")
data(Annotation_example)
data(seed_example)
alignmentDir <-
unlist(strsplit(dir(system.file("extdata",package="
pd
ProbeRemap"),
unlist(strsplit(dir(system.file("extdata",package="
array
ProbeRemap"),
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("
pd
ProbeRemap")
library("
array
ProbeRemap")
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 =
pd
ProbeRemap::makeOriginalPackageObject(originalAnnotationDir = dir1,
o1 =
array
ProbeRemap::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("
pd
ProbeRemap")
library("
array
ProbeRemap")
outDir <- "/Users/milchevs/ownCloud/ProbeRemapStep3/R/testdata/DroGene1_1"
OriginalAnnotDir <- "/Users/milchevs/Downloads/CD_DrosGenome1\ 2/Full/DrosGenome1/LibFiles/"
...
...
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