makeOriginalPackageObject: make original annotation object

In VladaMilch/pdProbeRemap: What the package does (short line)

Description

read in original array annotation

Usage

makeOriginalPackageObject(originalAnnotationDir,
  celFilePath = "InputFilePath", author = "Unknown", email = "un@known",
  pkgNameSUFFIX = ".originalPackage", organism, species, outputDir)

Arguments

originalAnnotationDir	directory that contains annotation files: ".pgf", ".clf", ".probeset.csv", ".mps" and ".transcript.csv" files, if annotation is PGF-based; ".cdf" – Chip Definition file, ".CEL" – example CEL file, "probe_tab" – tabulated .txt probes file
celFilePath	path to CEL file, if not present in originalAnnotationDir and annotation is CDF-based
author	character, author
email	character, email
pkgNameSUFFIX	character, suffix to package name
organism	character (ex: "Human")
species	character (ex: "Homo Sapiens")
outputDir	path to user-spesified output directory

Details

read in original array annotation from Affymetrix (CDF-based or PGF-based), and produce an object required for an annotation package, compatible with oligo or affy.

Value

a "output type".

Author(s)

Vladislava Milchevskaya [e-mail]

See Also

function or class name

Examples

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 )

VladaMilch/pdProbeRemap documentation built on May 28, 2019, 3:21 p.m.