# TARgeted SEQuencing Experiment Quality Control

## Documentation for package ‘TarSeqQC’ version 1.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C G I M O P R S T misc

TarSeqQC-package | TarSeqQC: Targeted Sequencing Experiment Quality Control R package

## -- A --

addStatSummSheet | TargetExperiment auxiliar function.
addStatSummSheet-method | TargetExperiment auxiliar function.
addStatSummSheet-methods | TargetExperiment auxiliar function.
ampliPanel | An amplicon panel example for use the TarSeqQC R package.
ampliPanel2 | An amplicon panel example for use the TarSeqQC R package.

## -- B --

biasExploration | Plot attribute density and boxplot for each bias source quartile or category.
biasExploration-method | Plot attribute density and boxplot for each bias source quartile or category.
biasExploration-methods | Plot attribute density and boxplot for each bias source quartile or category.
buildFeaturePanel | Function to build a feature panel based on specific genomic regions.
buildFeaturePanel-method | Function to build a feature panel based on specific genomic regions.
buildFeaturePanel-methods | Function to build a feature panel based on specific genomic regions.
buildReport | TargetExperiment auxiliar function.
buildReport-method | TargetExperiment auxiliar function.
buildReport-methods | TargetExperiment auxiliar function.

## -- C --

checkBedFasta | Function to control Bed and FASTA files compatibility.
checkBedFasta-methods | Function to control Bed and FASTA files compatibility.

## -- G --

getAttribute | Getters for TargetExperiment and TargetExperimentList objects.
getAttribute-method | Getters for TargetExperiment and TargetExperimentList objects.
getAttribute-methods | Getters for TargetExperiment and TargetExperimentList objects.
getBamFile | Getters for TargetExperiment and TargetExperimentList objects.
getBamFile-method | Getters for TargetExperiment and TargetExperimentList objects.
getBamFile-methods | Getters for TargetExperiment and TargetExperimentList objects.
getBedFile | Getters for TargetExperiment and TargetExperimentList objects.
getBedFile-method | Getters for TargetExperiment and TargetExperimentList objects.
getBedFile-methods | Getters for TargetExperiment and TargetExperimentList objects.
getFastaFile | Getters for TargetExperiment and TargetExperimentList objects.
getFastaFile-method | Getters for TargetExperiment and TargetExperimentList objects.
getFastaFile-methods | Getters for TargetExperiment and TargetExperimentList objects.
getFeature | Getters for TargetExperiment and TargetExperimentList objects.
getFeature-method | Getters for TargetExperiment and TargetExperimentList objects.
getFeature-methods | Getters for TargetExperiment and TargetExperimentList objects.
getFeaturePanel | Getters for TargetExperiment and TargetExperimentList objects.
getFeaturePanel-method | Getters for TargetExperiment and TargetExperimentList objects.
getFeaturePanel-methods | Getters for TargetExperiment and TargetExperimentList objects.
getGenePanel | Getters for TargetExperiment and TargetExperimentList objects.
getGenePanel-method | Getters for TargetExperiment and TargetExperimentList objects.
getGenePanel-methods | Getters for TargetExperiment and TargetExperimentList objects.
getLowCtsFeatures | Getters for TargetExperiment and TargetExperimentList objects.
getLowCtsFeatures-method | Getters for TargetExperiment and TargetExperimentList objects.
getLowCtsFeatures-methods | Getters for TargetExperiment and TargetExperimentList objects.
getOverlappedRegions | Getters for TargetExperiment and TargetExperimentList objects.
getOverlappedRegions-method | Getters for TargetExperiment and TargetExperimentList objects.
getPanels | Getters for TargetExperiment and TargetExperimentList objects.
getPanels-method | Getters for TargetExperiment and TargetExperimentList objects.
getPileupP | Getters for TargetExperiment and TargetExperimentList objects.
getPileupP-method | Getters for TargetExperiment and TargetExperimentList objects.
getPileupP-methods | Getters for TargetExperiment and TargetExperimentList objects.
getRegion | Getters for TargetExperiment and TargetExperimentList objects.
getRegion-method | Getters for TargetExperiment and TargetExperimentList objects.
getRegion-methods | Getters for TargetExperiment and TargetExperimentList objects.
getScanBamP | Getters for TargetExperiment and TargetExperimentList objects.
getScanBamP-method | Getters for TargetExperiment and TargetExperimentList objects.
getScanBamP-methods | Getters for TargetExperiment and TargetExperimentList objects.
ggplotColours | TargetExperiment auxiliar function.
ggplotColours-method | TargetExperiment auxiliar function.
ggplotColours-methods | TargetExperiment auxiliar function.

## -- I --

initialize | TargetExperiment object constructor.
initialize-method | TargetExperiment object constructor.
initialize-method | TargetExperimentList object constructor.

## -- M --

myCounts | A pileup matrix example for use the TarSeqQC R package.

## -- O --

Object | TargetExperiment and TargetExperimentList summary methods.
object | A set of two amplicon panels example for use the TarSeqQC R package.

## -- P --

pileupCounts | Function to obtain the pileup counts for a bam file.
pileupCounts-methods | Function to obtain the pileup counts for a bam file.
plot | Plot TargetExperiment object overview.
plot,TargetExperiment | Plot TargetExperiment object overview.
plot,TargetExperimentList | Plot TargetExperiment object overview.
plot.TargetExperiment | Plot TargetExperiment object overview.
plot.TargetExperimentList | Plot TargetExperiment object overview.
plotAttrExpl | Plot attribute exploration of a TargetExperiment/TargetExperimentList object.
plotAttrExpl-method | Plot attribute exploration of a TargetExperiment/TargetExperimentList object.
plotAttrExpl-methods | Plot attribute exploration of a TargetExperiment/TargetExperimentList object.
plotAttrPerform | Plot feature performance of a TargetExperiment object.
plotAttrPerform-method | Plot feature performance of a TargetExperiment object.
plotAttrPerform-methods | Plot feature performance of a TargetExperiment object.
plotFeatPerform | Plot feature performance of a TargetExperiment object.
plotFeatPerform-method | Plot feature performance of a TargetExperiment object.
plotFeatPerform-methods | Plot feature performance of a TargetExperiment object.
plotFeature | Plot read profiles for a particular feature.
plotFeature-method | Plot read profiles for a particular feature.
plotFeature-methods | Plot read profiles for a particular feature.
plotGeneAttrPerFeat | Plot the attribute value for all the features of a selected gene.
plotGeneAttrPerFeat-method | Plot the attribute value for all the features of a selected gene.
plotGeneAttrPerFeat-methods | Plot the attribute value for all the features of a selected gene.
plotGlobalAttrExpl | Plot attribute exploration of a TargetExperimentList object.
plotGlobalAttrExpl-method | Plot attribute exploration of a TargetExperimentList object.
plotGlobalAttrExpl-methods | Plot attribute exploration of a TargetExperimentList object.
plotInOutFeatures | Function to explore read percentages in targeted regions and out targeted regions.
plotInOutFeatures-method | Function to explore read percentages in targeted regions and out targeted regions.
plotMetaDataExpl | Graphical exploration of a specific metadata column.
plotMetaDataExpl-method | Graphical exploration of a specific metadata column.
plotMetaDataExpl-methods | Graphical exploration of a specific metadata column.
plotNtdPercentage | Plot nucleotide read percentages for a particular feature.
plotNtdPercentage-method | Plot nucleotide read percentages for a particular feature.
plotNtdPercentage-methods | Plot nucleotide read percentages for a particular feature.
plotPoolPerformance | Plot pool performance of a TargetExperimentList object.
plotPoolPerformance-method | Plot pool performance of a TargetExperimentList object.
plotPoolPerformance-methods | Plot pool performance of a TargetExperimentList object.
plotRegion | Plot read profiles for a particular genomic region.
plotRegion-method | Plot read profiles for a particular genomic region.
plotRegion-methods | Plot read profiles for a particular genomic region.
print | Print a TargetExperiment/TargetExperimentList object.
print-method | Print a TargetExperiment/TargetExperimentList object.

## -- R --

readFrequencies | Function to explore read frequencies in targeted regions and out targeted regions.
readFrequencies-method | Function to explore read frequencies in targeted regions and out targeted regions.
readFrequencies-methods | Function to explore read frequencies in targeted regions and out targeted regions.

## -- S --

setAttribute<- | Setters for the TargetExperiment slots
setAttribute<--method | Setters for the TargetExperiment slots
setAttribute<--methods | Setters for the TargetExperiment slots
setBamFile<- | Setters for the TargetExperiment slots
setBamFile<--method | Setters for the TargetExperiment slots
setBedFile<- | Setters for the TargetExperiment slots
setBedFile<--method | Setters for the TargetExperiment slots
setBedFile<--methods | Setters for the TargetExperiment slots
setFastaFile<- | Setters for the TargetExperiment slots
setFastaFile<--method | Setters for the TargetExperiment slots
setFastaFile<--methods | Setters for the TargetExperiment slots
setFeature<- | Setters for the TargetExperiment slots
setFeature<--method | Setters for the TargetExperiment slots
setFeature<--methods | Setters for the TargetExperiment slots
setFeaturePanel<- | Setters for the TargetExperiment slots
setFeaturePanel<--method | Setters for the TargetExperiment slots
setFeaturePanel<--methods | Setters for the TargetExperiment slots
setGenePanel<- | Setters for the TargetExperiment slots
setGenePanel<--method | Setters for the TargetExperiment slots
setGenePanel<--methods | Setters for the TargetExperiment slots
setPileupP<- | Setters for the TargetExperiment slots
setPileupP<--method | Setters for the TargetExperiment slots
setPileupP<--methods | Setters for the TargetExperiment slots
setScanBamP<- | Setters for the TargetExperiment slots
setScanBamP<--method | Setters for the TargetExperiment slots
setScanBamP<--methods | Setters for the TargetExperiment slots
setsetBamFile<- | Setters for the TargetExperiment slots
setsetBamFile<--methods | Setters for the TargetExperiment slots
show | Show method for the TargetExperiment and TargetExperimentList classes.
show-method | Show method for the TargetExperiment and TargetExperimentList classes.
summarizePanel | Function to summarize a featurePanel slot at a gene level.
summarizePanel-method | Function to summarize a featurePanel slot at a gene level.
summarizePanel-methods | Function to summarize a featurePanel slot at a gene level.
summary | TargetExperiment and TargetExperimentList summary methods.
summary(ampliPanel) | TargetExperiment and TargetExperimentList summary methods.
summary-method | TargetExperiment and TargetExperimentList summary methods.
summaryFeatureLev | TargetExperiment and TargetExperimentList summary methods.
summaryFeatureLev-method | TargetExperiment and TargetExperimentList summary methods.
summaryFeatureLev-methods | TargetExperiment and TargetExperimentList summary methods.
summaryGeneLev | TargetExperiment and TargetExperimentList summary methods.
summaryGeneLev-method | TargetExperiment and TargetExperimentList summary methods.
summaryGeneLev-methods | TargetExperiment and TargetExperimentList summary methods.
summaryIntervals | TargetExperiment and TargetExperimentList summary methods.
summaryIntervals-method | TargetExperiment and TargetExperimentList summary methods.
summaryIntervals-methods | TargetExperiment and TargetExperimentList summary methods.

## -- T --

TargetExperiment | TargetExperiment constructor
TargetExperiment-class | TargetExperiment S4 class implementation in R
TargetExperiment-methods | TargetExperiment constructor
TargetExperimentList | TargetExperimentList constructor
TargetExperimentList-class | TargetExperimentList S4 class implementation in R
TargetExperimentList-method | TargetExperimentList object constructor.
TargetExperimentList-methods | TargetExperimentList constructor
TEList | A set of two amplicon panels example for use the TarSeqQC R package.

## -- misc --

# | TargetExperiment and TargetExperimentList summary methods.