createSummarizedMatrix {blima} | R Documentation

## Summarized value matrix.

### 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)

Vojtěch 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').");
    }

[Package blima version 1.24.0 Index]