createSummarizedMatrix: Summarized value matrix.

In blima: Tools for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level

Description

This function creates summarized matrix of values of certain type.

Usage

createSummarizedMatrix(b, spotsToProcess = NULL, quality = "qua", 
    channelInclude = "bgf", annotationTag = NULL)

Arguments

b	List of beadLevelData objects (or single object).
spotsToProcess	NULL for processing all spots in b. Otherwise specifies logical vector of the length equals to the number of arrays in b.
quality	Quality to matrize.
channelInclude	This field allows user to set channel with weights which have to be from 0,1. All zero weighted items are excluded from summarization. You can turn this off by setting this NULL. This option may be used together with bacgroundCorrect method or/and with beadarray QC (defaults to "bgf").
annotationTag	Tag from annotation file which to use in resulting matrix as colname.

Author(s)

Vojt<c4><9b>ch Kulvait

Examples

if(require("blimaTestingData") && require("illuminaHumanv4.db") && interactive())
{
    #Create summarization of nonnormalized data from GrnF column.
    data(blimatesting)
    blimatesting = bacgroundCorrect(blimatesting, channelBackgroundFilter="bgf")
    blimatesting = nonPositiveCorrect(blimatesting, channelCorrect="GrnF",  channelBackgroundFilter="bgf", channelAndVector="bgf")
    #Prepare logical vectors corresponding to conditions A(groups1Mod), E(groups2Mod) and both(processingMod).
    nonnormalized = createSummarizedMatrix(blimatesting, quality="GrnF", channelInclude="bgf",
            annotationTag="Name")
    head(nonnormalized)
}else
{
    print("To run this example, please install blimaTestingData package from bioconductor by running BiocManager::install('blimaTestingData').");
}

blima documentation built on Nov. 8, 2020, 8:15 p.m.