## ---- message=FALSE------------------------------------------------------
library("pdProbeRemap")
## ---- eval = FALSE-------------------------------------------------------
# #evaluation worked
# dir1 = "/Users/milchevs/ownCloud/ProbeRemapSteps14/inst/extdata/mogene2_affyLibFiles_pgfBased/"
# outDir = "/Users/milchevs/ownCloud/ProbeRemapSteps14/OutPutDir/"
# dir.create(outDir)
#
# annotation2fasta(originalAnnotationDir = dir1,
# organism = "Mouse", species = "Mus musculus",
# author = "Vladislava Milchevskaya",
# email = "milchv@gmail.com",
# outputDir = outDir,
# reverse = FALSE)
## ---- eval = FALSE-------------------------------------------------------
# # evaluation worked
# path_to_STAR = "/path/to/STAR"
# sequence_fasta = "/path/to/sequence.fasta"
# genomeDir = "/path/to/reference/genome/"
# organism = "Human"
# outfile = "output_file."
#
# star.command.make(path_to_STAR, sequence_fasta, genomeDir, organism, outfile)
## ---- eval = FALSE------------------------------------------------------
# # evaluation worked
# outputDirAnotationDro <- "/Users/milchevs/Downloads/NewPackages/DroGene1_1"
#
# require("refGenome")
# beg <- ensemblGenome()
# basedir(beg) <- "/Users/milchevs/databases/sequences/Ensembl/annotation/Dmel/"
# ens_gtf <- "dmel-all-r6.09.gtf" # adjusted file, excessive white spaces deleted
# read.gtf(beg, ens_gtf)
# #tableAttributeTypes(beg)
# #moveAttributes(beg,c("gene_name","transcript_id","transcript_name","exon_number"))
#
# ANN_all.list <- (as.list(beg@ev))
# ANN_all <- ANN_all.list$gtf
# head(ANN_all)
# save(ANN_all, file = file.path(outputDirAnotationDro, paste0(ens_gtf, ".AnnotationDataFrame.RData")))
## ---- eval = FALSE-------------------------------------------------------
# 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")
# dir1 = "/Users/milchevs/ownCloud/ProbeRemapSteps14/inst/extdata/mogene2_affyLibFiles_pgfBased/"
# outDir = "/Users/milchevs/ownCloud/ProbeRemapSteps14/OutPutDir/"
# o1 = makeOriginalPackageObject(originalAnnotationDir = dir1,
# organism = "Mouse",
# species = "Mus musculus",
# outputDir = outDir )
#
# # NEW_ParsedData <- alignments2parsedData <- function(alignment.dir,
# # Annotation,
# # outputDir,
# # level,
# # min_probe_number,
# # package_seed)
#
#
# library("pdProbeRemap")
# data(Alignments_class_example, package = "pdProbeRemap")
# data(Annotation_example)
# data(seed_example)
# alignmentDir <-
# unlist(strsplit(dir(system.file("extdata",package="pdProbeRemap"),
# pattern="example_drosophila.Aligned.out.sam",
# full.names=TRUE), split = "example_drosophila.Aligned.out.sam"))[1]
#
#
# makeNewAnnotationPackage(alignment.dir = alignmentDir,
# Annotation = Annotation_example,
# outputDir = outDir,
# #outputDir = ".",
# level = "gene",
# min_probe_number = 1,
# pkgNameSUFFIX = ".example")
#
## ---- eval = FALSE-------------------------------------------------------
# library("pdProbeRemap")
#
# 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")
# dir1 = "/Users/milchevs/ownCloud/ProbeRemapSteps14/inst/extdata/mogene2_affyLibFiles_pgfBased/"
# outDir = "/Users/milchevs/ownCloud/ProbeRemapSteps14/OutPutDir/Probe_Sequences_Fasta/"
#
## ---- eval = FALSE-------------------------------------------------------
# o1 = pdProbeRemap::makeOriginalPackageObject(originalAnnotationDir = dir1,
# organism = "Mouse",
# species = "Mus musculus",
# outputDir = outDir )
## ---- eval = FALSE-------------------------------------------------------
# NEW_PD = makeNewAnnotationPackage(alignment.dir = alignmentDir,
# Annotation = ANN_MUS_all,
# outputDir = outDir,
# level = "gene",
# min_probe_number = 1,
# #package_seed = o1,
# quiet = FALSE,
# pkgNameSUFFIX = ".example")
# #
## ---- eval = FALSE-------------------------------------------------------
# CelFilesPath = c("/path/to/celfile1.CEL", "/path/to/celfile2.CEL")
# celfiles = read.celfiles(filenames=CelFilesPath,
# pkgname = "pd.mogene.2.0.st")
## ---- eval = FALSE-------------------------------------------------------
# install.packages("/path/to/new/pd/annotation/package/pd.NEWPACKAGE",
# repos=NULL, type="source")
# library("pd.NEWPACKAGE")
#
# CelFilesPath = c("/path/to/celfile1.CEL", "/path/to/celfile2.CEL")
# celfiles = read.celfiles(filenames=CelFilesPath,
# pkgname = "pd.NEWPACKAGE")
## ---- eval = FALSE-------------------------------------------------------
# library("pdProbeRemap")
#
# outDir <- "/Users/milchevs/ownCloud/ProbeRemapStep3/R/testdata/DroGene1_1"
# OriginalAnnotDir <- "/Users/milchevs/Downloads/CD_DrosGenome1\ 2/Full/DrosGenome1/LibFiles/"
#
# FastaFilePath_dro <- annotation2fasta(originalAnnotationDir = OriginalAnnotDir,
# organism = "Dmel",
# species = "Drosophila melanogaster",
# outputDir = outDir,
# author = "Name Surname",
# email = "e@mail",
# reverse = FALSE )
## ---- eval = FALSE-------------------------------------------------------
# ######### step 2 ###########
# # alignment #
# star_command_plainprobes =
# star.command.make(sequence_fasta = "/var/local/milchevs/ALIGNED/DroGene1/FASTA/DrosGenome1_probe_sequences_to_align.fasta", # the path is different because for helios!
# genomeDir = "/var/local/milchevs/databases/sequences/Ensembl/star/Dmel/",
# species = "Dmel",
# outfile = "/var/local/milchevs/ALIGNED/DroGene1/DrosGenome1.",
# runThreadN = 6)
#
# ######### step 3 ###########
# load("/Users/milchevs/Downloads/NewPackages/DroGene1_1/dmel-all-r6.09.gtf.AnnotationDataFrame.RData") # Annotation
# alignmentDir = file.path("/Users/milchevs/ownCloud/ProbeRemapStep3/R/testdata/DroGene1_1/", "Alignments")
#
# makeNewAnnotationPackage(alignment.dir = alignmentDir,
# Annotation = ANN_all,
# outputDir = outDir,
# level = "gene",
# min_probe_number = 1,
# quiet=FALSE,
# pkgNameSUFFIX = ".NewAnnotation"
# )
#
# install.packages("/Users/milchevs/ownCloud/ProbeRemapStep3/R/testdata/DroGene1_1/pd.drosgenome1.NewAnnotation/", repos = NULL, type = "source")
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