TargetExperiment-initialize: TargetExperiment object constructor.

In gamerino/TarSeqQC: TARgeted SEQuencing Experiment Quality Control

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 [e-mail], Cristobal Fresno [e-mail], Yanina Murua [e-mail], Andrea S. Llera [e-mail] and Elmer A. Fernandez [e-mail]

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)
}

gamerino/TarSeqQC documentation built on Feb. 3, 2020, 9:19 p.m.