TARgeted SEQuencing Experiment Quality Control


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Documentation for package ‘TarSeqQC’ version 1.2.0

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A B G I M O P R S T misc

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

-- A --

addStatSummSheet Build excel report of the Target Experiment.
addStatSummSheet-method Build excel report of the Target Experiment.
addStatSummSheet-methods Build excel report of the Target Experiment.
ampliPanel An amplicon panel example for use the TarSeqQC R package.

-- B --

biasExploration Plot attribute density and boxplot for each bias source quartile.
biasExploration-method Plot attribute density and boxplot for each bias source quartile.
biasExploration-methods Plot attribute density and boxplot for each bias source quartile.
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 Build excel report of the Target Experiment.
buildReport-method Build excel report of the Target Experiment.
buildReport-methods Build excel report of the Target Experiment.

-- G --

getAttribute Getters for TargetExperiment object.
getAttribute-method Getters for TargetExperiment object.
getAttribute-methods Getters for TargetExperiment object.
getBamFile Getters for TargetExperiment object.
getBamFile-method Getters for TargetExperiment object.
getBamFile-methods Getters for TargetExperiment object.
getBedFile Getters for TargetExperiment object.
getBedFile-method Getters for TargetExperiment object.
getBedFile-methods Getters for TargetExperiment object.
getFastaFile Getters for TargetExperiment object.
getFastaFile-method Getters for TargetExperiment object.
getFastaFile-methods Getters for TargetExperiment object.
getFeature Getters for TargetExperiment object.
getFeature-method Getters for TargetExperiment object.
getFeature-methods Getters for TargetExperiment object.
getFeaturePanel Getters for TargetExperiment object.
getFeaturePanel-method Getters for TargetExperiment object.
getFeaturePanel-methods Getters for TargetExperiment object.
getGenePanel Getters for TargetExperiment object.
getGenePanel-method Getters for TargetExperiment object.
getGenePanel-methods Getters for TargetExperiment object.
getLowCtsFeatures Getters for TargetExperiment object.
getLowCtsFeatures-method Getters for TargetExperiment object.
getLowCtsFeatures-methods Getters for TargetExperiment object.
getPileupP Getters for TargetExperiment object.
getPileupP-method Getters for TargetExperiment object.
getPileupP-methods Getters for TargetExperiment object.
getRegion Getters for TargetExperiment object.
getRegion-method Getters for TargetExperiment object.
getRegion-methods Getters for TargetExperiment object.
getScanBamP Getters for TargetExperiment object.
getScanBamP-method Getters for TargetExperiment object.
getScanBamP-methods Getters for TargetExperiment object.
ggplotColours Build excel report of the Target Experiment.
ggplotColours-method Build excel report of the Target Experiment.
ggplotColours-methods Build excel report of the Target Experiment.

-- I --

initialize TargetExperiment object constructor.
initialize-method TargetExperiment object constructor.

-- M --

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

-- O --

Object TargetExperiment summary.

-- 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-method Plot TargetExperiment object overview.
plotAttrExpl Plot attribute exploration of a TargetExperiment object.
plotAttrExpl-method Plot attribute exploration of a TargetExperiment object.
plotAttrExpl-methods Plot attribute exploration of a TargetExperiment 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.
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.
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 object.
print-method Print a TargetExperiment 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 class.
show-method Show method for the TargetExperiment class.
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 summary.
summary(ampliPanel) TargetExperiment summary.
summary-method TargetExperiment summary.
summaryFeatureLev TargetExperiment summary.
summaryFeatureLev-method TargetExperiment summary.
summaryFeatureLev-methods TargetExperiment summary.
summaryGeneLev TargetExperiment summary.
summaryGeneLev-method TargetExperiment summary.
summaryGeneLev-methods TargetExperiment summary.
summaryIntervals TargetExperiment summary.
summaryIntervals-method TargetExperiment summary.
summaryIntervals-methods TargetExperiment summary.

-- T --

TargetExperiment TargetExperiment constructor
TargetExperiment-class TargetExperiment S4 class implementation in R
TargetExperiment-methods TargetExperiment constructor

-- misc --

# TargetExperiment summary.