initialize {TarSeqQC} | R Documentation

## TargetExperiment object constructor.

### Description

`initialize` creates the TargetExperiment object architecture for the specified bed and alignment BAM files. If 'scanBamP' and/or 'pileupP' parameters are not specified, default values of their constructors will be used.

### Usage

    ## S4 method for signature 'TargetExperiment'
    initialize(.Object, bedFile, bamFile, fastaFile,
        scanBamP = NULL, pileupP = NULL, feature = NULL, attribute = NULL,
        BPPARAM = bpparam())

### Arguments

`.Object` | TargetExperiment class.
`bedFile` | Character indicating the bed file full path.
`bamFile` | Character indicating the alignment and index bam files full paths.
`fastaFile` | Character indicating the full path to the genome reference and index files.
`scanBamP` | ScanBamParam indicating the parameters for read the BAM file.
`pileupP` | PileupParam indicating the parameters for pileup building.
`feature` | Character indicating the name of the feature that will be explored (e.g 'amplicon', 'exon').
`attribute` | Character indicating the name of the attribute that will be explored. Should be 'coverage' or 'medianCounts'.
`BPPARAM` | An optional BiocParallelParam instance defining the parallel back-end to be used during evaluation.

### Value

TargetExperiment object.

### Note

see full example in `TargetExperiment-class`

### Author(s)

Gabriela A. Merino gmerino@bdmg.com.ar, Cristobal Fresno cfresno@bdmg.com.ar, Yanina Murua ymurua@leloir.org.ar, Andrea S. Llera allera@leloir.org.ar and Elmer A. Fernandez efernandez@bdmg.com.ar

### See Also

`TargetExperiment`, `buildFeaturePanel` `summarizePanel`

Other TargetExperiment: `TargetExperiment-class`, `TargetExperiment`, `ampliPanel2`, `ampliPanel`, `myCounts`

### Examples

    ## Defining bam file, bed file and fasta file names and paths
    if(interactive()){
    bamFile<-system.file("extdata", "mybam.bam", package="TarSeqQC",
        mustWork=TRUE)
    bedFile<-system.file("extdata", "mybed.bed", package="TarSeqQC",
        mustWork=TRUE)
    fastaFile<-system.file("extdata", "myfasta.fa", package="TarSeqQC",
        mustWork=TRUE)

    ## Creating a TargetExperiment object

    ## Defining feature parameter
    feature<-"amplicon"
    ## Defining attribute parameter
    attribute<-"coverage"
    ##Calling the constructor
    ampliPanel<-TargetExperiment(bedFile, bamFile, fastaFile,
        attribute=attribute, feature=feature)
    }

[Package TarSeqQC version 1.10.0 Index]