maPreproc: Preprocessing of microarray expression data

Description Usage Arguments Value Author(s) See Also Examples

View source: R/geo2kegg.R

Description

This function prepares datasets of the GEO2KEGG microarray compendium for further analysis. This includes summarization of probe level expression to gene level expression as well as annotation of required colData slots for sample grouping.

Usage

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maPreproc(exp.list, parallel = NULL)

Arguments

exp.list

Experiment list. A list of datasets, each being of class ExpressionSet.

parallel

Parallel computation mode. An instance of class BiocParallelParam. See the vignette of the BiocParallel package for switching between serial, multi-core, and grid execution. Defaults to NULL, which then uses the first element of BiocParallel::registered() for execution. If not changed by the user, this accordingly defaults to multi-core execution on the local host.

Value

A list of datasets, each being of class SummarizedExperiment.

Author(s)

Ludwig Geistlinger <Ludwig.Geistlinger@sph.cuny.edu>

See Also

loadEData to load a specified expression data compendium.

Examples

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    # reading user-defined expression data from file
    geo2kegg <- loadEData("geo2kegg", nr.datasets=3)

    # only considering the first 100 probes for demonstration
    geo2kegg <- lapply(geo2kegg, function(d) d[1:100,])   

    # preprocessing two datasets
    geo2kegg <- maPreproc(geo2kegg[2:3])

waldronlab/GSEABenchmarkeR documentation built on Jan. 23, 2022, 10:02 p.m.