TargetExperiment {TarSeqQC} | R Documentation |
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.
TargetExperiment(bedFile, bamFile, fastaFile, scanBamP = NULL, pileupP = NULL, feature = NULL, attribute = NULL, BPPARAM = bpparam())
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. |
TargetExperiment object.
see full example in TargetExperiment-class
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
Other TargetExperiment: TargetExperiment-class
,
ampliPanel2
, ampliPanel
,
initialize
, myCounts
## 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)