TARgeted SEQuencing Experiment Quality Control

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Documentation for package ‘TarSeqQC’ version 1.10.0

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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.