TarSeqQC (version 1.2.0)

TargetExperiment: TargetExperiment constructor

Description

TargetExperiment creates a TargetExperiment object with the architecture specified by the bed and alingment 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 setted 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.

See Also

TargetExperiment-class1

Other TargetExperiment: TargetExperiment-class; ampliPanel; initialize, initialize,TargetExperiment-method

Examples

if (interactive()) {
## 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)
}