createOrLoadAnnotations: createOrLoadAnnotations

In uebvhir/BasicP4microArrays: Functions to create and run simple-to-complex microarray analysis pipeline

Description

Function that creates the annotation needed, or if it is already done, loads the file created. The annotation packages used need to be installed previously.

Usage

createOrLoadAnnotations(loadAnnotations = FALSE, chipPackAvailable,
  platformDesignPackAvailable, chipPackage, platformDesignPackage,
  outputDir, annotationsFileName, entrezTableFileName,
  symbolsTableFileName, controlsTableFileName)

Arguments

loadAnnotations	FALSE by default. If TRUE the function loads the annotations files.
chipPackAvailable	TRUE if there is a chip package available.
platformDesignPackAvailable	TRUE if there is a platform design package available.
chipPackage	Name of the chip package. Only if chipPackAvailable is TRUE.
platformDesignPackage	Name of the platform design. Only if platformDesignPackAvailable is TRUE.
outputDir	Path where the annotation will be stored.
annotationsFileName	Name of the file for annotations.
entrezTableFileName	Name of the file for Entrez genes.
symbolsTableFileName	Name of the file for gene symbols ID.
controlsTableFileName	Name of the file for controls.

Value

A list "anotacions" that contains the annotations, the Entrez genes and the gene symbols ID.

Examples

## Not run: 
loadAnnotations <- FALSE
chipPackAvailable <- TRUE
platformDesignPackAvailable <- FALSE
chipPackage <- "hgu133a2"
platformDesignPackage <- NULL
outputDir <- "./ResultsDir"
annotationsFileName <- "Annotations"
entrezTableFileName <-"Entrezs.Rda"
symbolsTableFileName <-"Symbols.Rda"
controlsTableFileName <- "controls.Rda"


anotacions <- createOrLoadAnnotations (loadAnnotations= loadAnnotations,
chipPackAvailable = chipPackAvailable, platformDesignPackAvailable = platformDesignPackAvailable,
chipPackage = chipPackage, platformDesignPackage = platformDesignPackage,
outputDir = outputDir,annotationsFileName = annotationsFileName,
entrezTableFileName = entrezTableFileName, symbolsTableFileName = symbolsTableFileName,
 controlsTableFileName = controlsTableFileName)
## End(Not run)

uebvhir/BasicP4microArrays documentation built on Nov. 5, 2019, 11:03 a.m.