addUpdatedCDFenv: Load an updated cdf environment from BrainArray

In ammar257ammar/ArrayAnalysis-Bioconductor: ArrayAnalysis

Load an updated cdf environment from BrainArray

Description

This function (from functions_processing) tries to find and load an updated cdf environment from BrainArray for the current chiptype. If this is not successful, a warning will be generated and the raw data object returned as is, i.e. with the cdf annotation that it already had, if any. Note that the IDs given to the reporters are artificially created by adding “_at” as a postfix to the ID from the entry in the database that the probeset corresponds to (c.f. also createNormDataTable). Note also that reannotation takes places at a probe level, not at a probeset level. This means that completely new probesets are constructed, not necessarily equal in size.

Usage

addUpdatedCDFenv(Data, species = NULL, type = "ENSG")

Arguments

Data	(Status: required) The raw data object (datatype: AffyBatch)
species	(Status: required, Default: NULL) The species associated with the chip type (datatype: character). Possible values: - Abbreviated: "Ag", "At", "Bt", "Ce", "Cf", "Dr", "Dm", "Gg", "Hs", "MAmu", "Mm", "Os", "Rn", "Sc", "Sp", "Ss" - Full names: "Anopheles gambiae", "Arabidopsis thaliana", "Bos taurus", "Caenorhabditis elegans", "Canis familiaris", "Danio rerio", "Drosophila melanogaster", "Gallus gallus", "Homo sapiens", "Macaca mulatta", "Mus musculus", "Oryza sativa", "Rattus norvegicus", "Saccharomyces cerevisiae", "Schizosaccharomyces pombe", "Sus scrofa".
type	(Status: optional, Default: "ENSG") The type of custom cdf requested This parameter indicates the database based on which an updated cdf environment should be selected (datatype: character). Possible values are: "ENTREZG", "REFSEQ", "ENSG", "ENSE", "ENST", "VEGAG", "VEGAE", "VEGAT", "TAIRG", "TAIRT", "UG", "MIRBASEF", "MIRBASEG".

Value

The object (of class AffyBatch) with a updated cdf annotation assigned if found

Examples

#By default, the script will call, if customCDF is TRUE
#(from within the \link[ArrayAnalysis]{normalizeData}
#and \link[ArrayAnalysis]{computePMAtable} functions,
#leaving the original Data intact and using Data.copy to further process):
#Data.copy <- Data
#Data.copy <- addUpdatedCDFenv(Data.copy, species, CDFtype)

ammar257ammar/ArrayAnalysis-Bioconductor documentation built on Jan. 29, 2024, 7:21 a.m.