TargetExperiment-constructor: TargetExperiment constructor

In TarSeqQC: TARgeted SEQuencing Experiment Quality Control

Description

TargetExperiment creates a TargetExperiment object with the architecture specified by the bed and alignment BAM files. If 'scanBamP' and/or 'pileupP' parameters are not specified, default values of their constructors will be used. attribute and feature parameters can be set after constructor calling.

Usage

TargetExperiment(bedFile, bamFile, fastaFile, scanBamP = NULL,
    pileupP = NULL, feature = NULL, attribute = NULL, BPPARAM = bpparam())

Arguments

bedFile	Character indicating the bed file full path.
bamFile	Character indicating the alignment and index bam files full path.
fastaFile	Character indicating the full path to the genome reference and index files.
scanBamP	ScanBamParam indicating the parameters the BAM file read.
pileupP	PileupParam indicating the parameters for the pileup build.
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-class1

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

Examples

## Defining bam file, bed file and fasta file names and paths
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
object<-TargetExperiment(bedFile, bamFile, fastaFile, attribute=attribute,
feature=feature)

TarSeqQC documentation built on Nov. 8, 2020, 6:03 p.m.