TarSeqQC-package | TarSeqQC: Targeted Sequencing Experiment Quality Control R package |
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. |
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. |
checkBedFasta | Function to control Bed and FASTA files compatibility. |
checkBedFasta-methods | Function to control Bed and FASTA files compatibility. |
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. |
initialize | TargetExperiment object constructor. |
initialize-method | TargetExperiment object constructor. |
initialize-method | TargetExperimentList object constructor. |
myCounts | A pileup matrix example for use the TarSeqQC R package. |
Object | TargetExperiment and TargetExperimentList summary methods. |
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. |
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 a TargetExperiment/TargetExperimentList object. | |
print-method | Print a TargetExperiment/TargetExperimentList object. |
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. |
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. |
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. |
# | TargetExperiment and TargetExperimentList summary methods. |