TEList                  A set of two amplicon panels example for use
                        the TarSeqQC R package.
TarSeqQC-package        TarSeqQC: Targeted Sequencing Experiment
                        Quality Control R package
TargetExperiment        TargetExperiment constructor
TargetExperiment-class
                        TargetExperiment S4 class implementation in R
TargetExperimentList    TargetExperimentList constructor
TargetExperimentList-class
                        TargetExperimentList S4 class implementation in
                        R
ampliPanel              An amplicon panel example for use the TarSeqQC
                        R package.
ampliPanel2             An amplicon panel example for use the TarSeqQC
                        R package.
biasExploration         Plot attribute density and boxplot for each
                        bias source quartile or category.
buildFeaturePanel       Function to build a feature panel based on
                        specific genomic regions.
buildReport             TargetExperiment auxiliar function.
checkBedFasta           Function to control Bed and FASTA files
                        compatibility.
getBedFile              Getters for TargetExperiment and
                        TargetExperimentList objects.
initialize              TargetExperiment object constructor.
initialize,TargetExperimentList-method
                        TargetExperimentList object constructor.
myCounts                A pileup matrix example for use the TarSeqQC R
                        package.
object                  A set of two amplicon panels example for use
                        the TarSeqQC R package.
pileupCounts            Function to obtain the pileup counts for a bam
                        file.
plot                    Plot TargetExperiment object overview.
plotAttrExpl            Plot attribute exploration of a
                        TargetExperiment/TargetExperimentList object.
plotAttrPerform         Plot feature performance of a TargetExperiment
                        object.
plotFeatPerform         Plot feature performance of a TargetExperiment
                        object.
plotFeature             Plot read profiles for a particular feature.
plotGeneAttrPerFeat     Plot the attribute value for all the features
                        of a selected gene.
plotGlobalAttrExpl      Plot attribute exploration of a
                        TargetExperimentList object.
plotInOutFeatures       Function to explore read percentages in
                        targeted regions and out targeted regions.
plotMetaDataExpl        Graphical exploration of a specific metadata
                        column.
plotNtdPercentage       Plot nucleotide read percentages for a
                        particular feature.
plotPoolPerformance     Plot pool performance of a TargetExperimentList
                        object.
plotRegion              Plot read profiles for a particular genomic
                        region.
print                   Print a TargetExperiment/TargetExperimentList
                        object.
readFrequencies         Function to explore read frequencies in
                        targeted regions and out targeted regions.
setFeature<-            Setters for the TargetExperiment slots
show                    Show method for the TargetExperiment and
                        TargetExperimentList classes.
summarizePanel          Function to summarize a featurePanel slot at a
                        gene level.
summaryFeatureLev       TargetExperiment and TargetExperimentList
                        summary methods.
