TarSeqQC: TARgeted SEQuencing Experiment Quality Control

The package allows the representation of targeted experiment in R. This is based on current packages and incorporates functions to do a quality control over this kind of experiments and a fast exploration of the sequenced regions. An xlsx file is generated as output.

AuthorGabriela A. Merino, Cristobal Fresno, Yanina Murua, Andrea S. Llera and Elmer A. Fernandez
Date of publicationNone
MaintainerGabriela Merino <gmerino@bdmg.com.ar>
LicenseGPL (>=2)
Version1.4.1
http://www.bdmg.com.ar

View on Bioconductor

Man pages

ampliPanel: An amplicon panel example for use the TarSeqQC R package.

ampliPanel2: An amplicon panel example for use the TarSeqQC R package.

checkBedFasta: Function to control Bed and FASTA files compatibility.

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

object: A set of two amplicon panels example for use the TarSeqQC R...

pileupCounts: Function to obtain the pileup counts for a bam file.

plotInOutFeatures: Function to explore read percentages in targeted regions and...

TargetExperiment-biasExploration: Plot attribute density and boxplot for each bias source...

TargetExperiment-buildFeaturePanel: Function to build a feature panel based on specific genomic...

TargetExperiment-buildReport: TargetExperiment auxiliar function.

TargetExperiment-class: TargetExperiment S4 class implementation in R

TargetExperiment-constructor: TargetExperiment constructor

TargetExperiment-getters: Getters for TargetExperiment and TargetExperimentList...

TargetExperiment-initialize: TargetExperiment object constructor.

TargetExperimentList-class: TargetExperimentList S4 class implementation in R

TargetExperimentList-constructor: TargetExperimentList constructor

TargetExperimentList-initialize: TargetExperimentList object constructor.

TargetExperimentList-plotGlobalAttrExpl: Plot attribute exploration of a TargetExperimentList object.

TargetExperimentList-plotPoolPerformance: Plot pool performance of a TargetExperimentList object.

TargetExperiment-plot: Plot TargetExperiment object overview.

TargetExperiment-plotAttrExpl: Plot attribute exploration of a...

TargetExperiment-plotAttrPerform: Plot feature performance of a TargetExperiment object.

TargetExperiment-plotFeatPerform: Plot feature performance of a TargetExperiment object.

TargetExperiment-plotFeature: Plot read profiles for a particular feature.

TargetExperiment-plotGeneAttrPerFeat: Plot the attribute value for all the features of a selected...

TargetExperiment-plotMetaDataExpl: Graphical exploration of a specific metadata column.

TargetExperiment-plotNtdPercentage: Plot nucleotide read percentages for a particular feature.

TargetExperiment-plotRegion: Plot read profiles for a particular genomic region.

TargetExperiment-print: Print a TargetExperiment/TargetExperimentList object.

TargetExperiment-readFrequencies: Function to explore read frequencies in targeted regions and...

TargetExperiment-setters: Setters for the TargetExperiment slots

TargetExperiment-show: Show method for the TargetExperiment and TargetExperimentList...

TargetExperiment-statistics: TargetExperiment and TargetExperimentList summary methods.

TargetExperiment-summarizePanel: Function to summarize a featurePanel slot at a gene level.

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

TEList: A set of two amplicon panels example for use the TarSeqQC R...

Functions

# Man page
addStatSummSheet Man page
addStatSummSheet-methods Man page
addStatSummSheet,TargetExperiment-method Man page
ampliPanel Man page
ampliPanel2 Man page
biasExploration Man page
biasExploration-methods Man page
biasExploration,TargetExperiment-method Man page
buildFeaturePanel Man page
buildFeaturePanel-methods Man page
buildFeaturePanel,TargetExperiment-method Man page
buildReport Man page
buildReport-methods Man page
buildReport,TargetExperiment-method Man page
checkBedFasta Man page
checkBedFasta-methods Man page
getAttribute Man page
getAttribute-methods Man page
getAttribute,TargetExperimentList-method Man page
getAttribute,TargetExperiment-method Man page
getBamFile Man page
getBamFile-methods Man page
getBamFile,TargetExperiment-method Man page
getBedFile Man page
getBedFile-methods Man page
getBedFile,TargetExperimentList-method Man page
getBedFile,TargetExperiment-method Man page
getFastaFile Man page
getFastaFile-methods Man page
getFastaFile,TargetExperiment-method Man page
getFeature Man page
getFeature-methods Man page
getFeaturePanel Man page
getFeaturePanel-methods Man page
getFeaturePanel,TargetExperiment-method Man page
getFeature,TargetExperimentList-method Man page
getFeature,TargetExperiment-method Man page
getGenePanel Man page
getGenePanel-methods Man page
getGenePanel,TargetExperiment-method Man page
getLowCtsFeatures Man page
getLowCtsFeatures-methods Man page
getLowCtsFeatures,TargetExperimentList-method Man page
getLowCtsFeatures,TargetExperiment-method Man page
getOverlappedRegions Man page
getOverlappedRegions,TargetExperiment-method Man page
getPanels Man page
getPanels,TargetExperimentList-method Man page
getPileupP Man page
getPileupP-methods Man page
getPileupP,TargetExperiment-method Man page
getRegion Man page
getRegion-methods Man page
getRegion,TargetExperimentList-method Man page
getRegion,TargetExperiment-method Man page
getScanBamP Man page
getScanBamP-methods Man page
getScanBamP,TargetExperiment-method Man page
ggplotColours Man page
ggplotColours-methods Man page
ggplotColours,TargetExperimentList-method Man page
ggplotColours,TargetExperiment-method Man page
initialize Man page
initialize,TargetExperimentList-method Man page
initialize,TargetExperiment-method Man page
myCounts Man page
object Man page
Object Man page
pileupCounts Man page
pileupCounts-methods Man page
plot Man page
plotAttrExpl Man page
plotAttrExpl-methods Man page
plotAttrExpl,TargetExperimentList-method Man page
plotAttrExpl,TargetExperiment-method Man page
plotAttrPerform Man page
plotAttrPerform-methods Man page
plotAttrPerform,TargetExperiment-method Man page
plotFeatPerform Man page
plotFeatPerform-methods Man page
plotFeatPerform,TargetExperiment-method Man page
plotFeature Man page
plotFeature-methods Man page
plotFeature,TargetExperiment-method Man page
plotGeneAttrPerFeat Man page
plotGeneAttrPerFeat-methods Man page
plotGeneAttrPerFeat,TargetExperiment-method Man page
plotGlobalAttrExpl Man page
plotGlobalAttrExpl-methods Man page
plotGlobalAttrExpl,TargetExperimentList-method Man page
plotInOutFeatures Man page
plotInOutFeatures,data.frame-method Man page
plotInOutFeatures,TargetExperiment-method Man page
plotMetaDataExpl Man page
plotMetaDataExpl-methods Man page
plotMetaDataExpl,TargetExperiment-method Man page
plotNtdPercentage Man page
plotNtdPercentage-methods Man page
plotNtdPercentage,TargetExperiment-method Man page
plotPoolPerformance Man page
plotPoolPerformance-methods Man page
plotPoolPerformance,TargetExperimentList-method Man page
plotRegion Man page
plotRegion-methods Man page
plotRegion,TargetExperiment-method Man page
plot,TargetExperiment Man page
plot.TargetExperiment Man page
plot,TargetExperimentList Man page
plot.TargetExperimentList Man page
print Man page
print,TargetExperimentList-method Man page
print,TargetExperiment-method Man page
readFrequencies Man page
readFrequencies-methods Man page
readFrequencies,TargetExperiment-method Man page
setAttribute<- Man page
setAttribute<--methods Man page
setAttribute<-,TargetExperiment,character-method Man page
setBamFile<- Man page
setBamFile<-,TargetExperiment,character-method Man page
setBedFile<- Man page
setBedFile<--methods Man page
setBedFile<-,TargetExperiment,character-method Man page
setFastaFile<- Man page
setFastaFile<--methods Man page
setFastaFile<-,TargetExperiment,character-method Man page
setFeature<- Man page
setFeature<--methods Man page
setFeaturePanel<- Man page
setFeaturePanel<--methods Man page
setFeaturePanel<-,TargetExperiment,GRanges-method Man page
setFeature<-,TargetExperiment,character-method Man page
setFeature<-,TargetExperimentList,character-method Man page
setGenePanel<- Man page
setGenePanel<--methods Man page
setGenePanel<-,TargetExperiment,GRanges-method Man page
setPileupP<- Man page
setPileupP<--methods Man page
setPileupP<-,TargetExperiment,PileupParam-method Man page
setScanBamP<- Man page
setScanBamP<--methods Man page
setScanBamP<-,TargetExperiment,ScanBamParam-method Man page
setsetBamFile<- Man page
setsetBamFile<--methods Man page
show Man page
show,TargetExperimentList-method Man page
show,TargetExperiment-method Man page
summarizePanel Man page
summarizePanel-methods Man page
summarizePanel,TargetExperiment-method Man page
summary Man page
summary(ampliPanel) Man page
summaryFeatureLev Man page
summaryFeatureLev-methods Man page
summaryFeatureLev,TargetExperiment-method Man page
summaryGeneLev Man page
summaryGeneLev-methods Man page
summaryGeneLev,TargetExperiment-method Man page
summaryIntervals Man page
summaryIntervals-methods Man page
summaryIntervals,TargetExperimentList-method Man page
summaryIntervals,TargetExperiment-method Man page
summary,TargetExperimentList-method Man page
summary,TargetExperiment-method Man page
TargetExperiment Man page
TargetExperiment-class Man page
TargetExperimentList Man page
TargetExperimentList-class Man page
TargetExperimentList-method Man page
TargetExperimentList-methods Man page
TargetExperiment-methods Man page
TarSeqQC-package Man page
TEList Man page

Files

TarSeqQC/DESCRIPTION
TarSeqQC/NAMESPACE
TarSeqQC/NEWS
TarSeqQC/R
TarSeqQC/R/TarSeqQC-package.R TarSeqQC/R/TargetExperiment-addStatSummSheet.R TarSeqQC/R/TargetExperiment-ampliPanel.R TarSeqQC/R/TargetExperiment-ampliPanel2.R TarSeqQC/R/TargetExperiment-biasExploration.R TarSeqQC/R/TargetExperiment-buildFeaturePanel.R TarSeqQC/R/TargetExperiment-buildReport.R TarSeqQC/R/TargetExperiment-constructor.R TarSeqQC/R/TargetExperiment-getters.R TarSeqQC/R/TargetExperiment-ggplotColours.R TarSeqQC/R/TargetExperiment-initialize.R TarSeqQC/R/TargetExperiment-myCounts.R TarSeqQC/R/TargetExperiment-pileupCounts.R TarSeqQC/R/TargetExperiment-plot.R TarSeqQC/R/TargetExperiment-plotAttrExpl.R TarSeqQC/R/TargetExperiment-plotAttrPerform.R TarSeqQC/R/TargetExperiment-plotFeatPerform.R TarSeqQC/R/TargetExperiment-plotFeature.R TarSeqQC/R/TargetExperiment-plotGeneAttrPerFeat.R TarSeqQC/R/TargetExperiment-plotInOutFeatures.R TarSeqQC/R/TargetExperiment-plotMetaDataExpl.R TarSeqQC/R/TargetExperiment-plotNtdPercentage.R TarSeqQC/R/TargetExperiment-plotRegion.R TarSeqQC/R/TargetExperiment-print.R TarSeqQC/R/TargetExperiment-readFrequencies.R TarSeqQC/R/TargetExperiment-setters.R TarSeqQC/R/TargetExperiment-show.R TarSeqQC/R/TargetExperiment-statistics.R TarSeqQC/R/TargetExperiment-summarizePanel.R TarSeqQC/R/TargetExperiment.R TarSeqQC/R/TargetExperimentList-TEList.R TarSeqQC/R/TargetExperimentList-constructor.R TarSeqQC/R/TargetExperimentList-getters.R TarSeqQC/R/TargetExperimentList-initialize.R TarSeqQC/R/TargetExperimentList-plot.R TarSeqQC/R/TargetExperimentList-plotAttrExpl.R TarSeqQC/R/TargetExperimentList-plotGlobalAttrExpl.R TarSeqQC/R/TargetExperimentList-plotPoolPerformance.R TarSeqQC/R/TargetExperimentList-print.R TarSeqQC/R/TargetExperimentList-setters.R TarSeqQC/R/TargetExperimentList-show.R TarSeqQC/R/TargetExperimentList-statistics.R TarSeqQC/R/TargetExperimentList.R TarSeqQC/R/checkBedFasta.R
TarSeqQC/build
TarSeqQC/build/vignette.rds
TarSeqQC/data
TarSeqQC/data/TEList.rda
TarSeqQC/data/ampliPanel.rda
TarSeqQC/data/ampliPanel2.rda
TarSeqQC/data/myCounts.rda
TarSeqQC/inst
TarSeqQC/inst/doc
TarSeqQC/inst/doc/TarSeqQC-vignette.R
TarSeqQC/inst/doc/TarSeqQC-vignette.Rnw
TarSeqQC/inst/doc/TarSeqQC-vignette.pdf
TarSeqQC/inst/extdata
TarSeqQC/inst/extdata/mybam.bam
TarSeqQC/inst/extdata/mybam.bam.bai
TarSeqQC/inst/extdata/mybed.bed
TarSeqQC/inst/extdata/myfasta.fa
TarSeqQC/inst/extdata/myfasta.fa.fai
TarSeqQC/inst/extdata/plot.pdf
TarSeqQC/inst/unitTests
TarSeqQC/inst/unitTests/test_TarSeqQC.R
TarSeqQC/man
TarSeqQC/man/TEList.Rd TarSeqQC/man/TarSeqQC-package.Rd TarSeqQC/man/TargetExperiment-biasExploration.Rd TarSeqQC/man/TargetExperiment-buildFeaturePanel.Rd TarSeqQC/man/TargetExperiment-buildReport.Rd TarSeqQC/man/TargetExperiment-class.Rd TarSeqQC/man/TargetExperiment-constructor.Rd TarSeqQC/man/TargetExperiment-getters.Rd TarSeqQC/man/TargetExperiment-initialize.Rd TarSeqQC/man/TargetExperiment-plot.Rd TarSeqQC/man/TargetExperiment-plotAttrExpl.Rd TarSeqQC/man/TargetExperiment-plotAttrPerform.Rd TarSeqQC/man/TargetExperiment-plotFeatPerform.Rd TarSeqQC/man/TargetExperiment-plotFeature.Rd TarSeqQC/man/TargetExperiment-plotGeneAttrPerFeat.Rd TarSeqQC/man/TargetExperiment-plotMetaDataExpl.Rd TarSeqQC/man/TargetExperiment-plotNtdPercentage.Rd TarSeqQC/man/TargetExperiment-plotRegion.Rd TarSeqQC/man/TargetExperiment-print.Rd TarSeqQC/man/TargetExperiment-readFrequencies.Rd TarSeqQC/man/TargetExperiment-setters.Rd TarSeqQC/man/TargetExperiment-show.Rd TarSeqQC/man/TargetExperiment-statistics.Rd TarSeqQC/man/TargetExperiment-summarizePanel.Rd TarSeqQC/man/TargetExperimentList-class.Rd TarSeqQC/man/TargetExperimentList-constructor.Rd TarSeqQC/man/TargetExperimentList-initialize.Rd TarSeqQC/man/TargetExperimentList-plotGlobalAttrExpl.Rd TarSeqQC/man/TargetExperimentList-plotPoolPerformance.Rd TarSeqQC/man/ampliPanel.Rd TarSeqQC/man/ampliPanel2.Rd TarSeqQC/man/checkBedFasta.Rd TarSeqQC/man/myCounts.Rd TarSeqQC/man/object.Rd TarSeqQC/man/pileupCounts.Rd TarSeqQC/man/plotInOutFeatures.Rd
TarSeqQC/tests
TarSeqQC/tests/runTests.R
TarSeqQC/vignettes
TarSeqQC/vignettes/GlobalAttrPool.pdf
TarSeqQC/vignettes/NTDPercAMPL20.pdf
TarSeqQC/vignettes/RETRegion.pdf
TarSeqQC/vignettes/TEList.pdf
TarSeqQC/vignettes/TarSeqQC-vignette.Rnw
TarSeqQC/vignettes/TarSeqQCvignette.bib
TarSeqQC/vignettes/attrExpl.pdf
TarSeqQC/vignettes/attrPerfPool.pdf
TarSeqQC/vignettes/attrPerfPoolThres.pdf
TarSeqQC/vignettes/authblk.sty
TarSeqQC/vignettes/class.pdf
TarSeqQC/vignettes/coveragePerform.pdf
TarSeqQC/vignettes/featPerf.pdf
TarSeqQC/vignettes/featuregene7.pdf
TarSeqQC/vignettes/framed.sty
TarSeqQC/vignettes/gcExploration.pdf
TarSeqQC/vignettes/gene2Exploration.pdf
TarSeqQC/vignettes/gene4AttrFeat.pdf
TarSeqQC/vignettes/gene7Region.pdf
TarSeqQC/vignettes/geneAttrPerFeatOverlap.pdf
TarSeqQC/vignettes/geneExploration.pdf
TarSeqQC/vignettes/lengthExploration.pdf
TarSeqQC/vignettes/perfExplCCP.pdf
TarSeqQC/vignettes/plot.pdf
TarSeqQC/vignettes/plotCPP.pdf
TarSeqQC/vignettes/plotInOut.pdf
TarSeqQC/vignettes/plotNoLab.pdf
TarSeqQC/vignettes/plotTEList.pdf
TarSeqQC/vignettes/poolPerformDens.pdf
TarSeqQC/vignettes/poolPerformThres.pdf

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