TargetExperiment-constructor: TargetExperiment constructor

Description Usage Arguments Value Note Author(s) See Also Examples

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

1
2
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 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-class1

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

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
## 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)

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