initialize {TarSeqQC} | R Documentation |
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.
## S4 method for signature 'TargetExperiment' initialize(.Object, bedFile, bamFile, fastaFile, scanBamP = NULL, pileupP = NULL, feature = NULL, attribute = NULL, BPPARAM = bpparam())
.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. |
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
TargetExperiment
, buildFeaturePanel
summarizePanel
Other TargetExperiment: TargetExperiment-class
,
TargetExperiment
,
ampliPanel2
, ampliPanel
,
myCounts
## 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) }