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TarSeqQC (version 1.2.0)

TARgeted SEQuencing Experiment Quality Control

Description

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.

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Version

Version

1.2.0

License

GPL (>=2)

Maintainer

Gabriela Merino

Last Published

February 15th, 2017

Functions in TarSeqQC (1.2.0)

print

Print a TargetExperiment object.
addStatSummSheet

Build excel report of the Target Experiment.
getBedFile

Getters for TargetExperiment object.
pileupCounts

Function to obtain the pileup counts for a bam file.
buildFeaturePanel

Function to build a feature panel based on specific genomic regions.
summaryFeatureLev

TargetExperiment summary.
plot

Plot TargetExperiment object overview.
show

Show method for the TargetExperiment class.
myCounts

A pileup matrix example for use the TarSeqQC R package.
setFeature<-

Setters for the TargetExperiment slots
plotAttrExpl

Plot attribute exploration of a TargetExperiment object.
plotFeatPerform

Plot feature performance of a TargetExperiment object.
plotRegion

Plot read profiles for a particular genomic region.
TargetExperiment

TargetExperiment constructor
plotMetaDataExpl

Graphical exploration of a specific metadata column.
TargetExperiment-class

TargetExperiment S4 class implementation in R
plotNtdPercentage

Plot nucleotide read percentages for a particular feature.
biasExploration

Plot attribute density and boxplot for each bias source quartile.
plotFeature

Plot read profiles for a particular feature.
ampliPanel

An amplicon panel example for use the TarSeqQC R package.
plotInOutFeatures

Function to explore read percentages in targeted regions and out targeted regions.
TarSeqQC-package

TarSeqQC: Targeted Sequencing Experiment Quality Control R package
readFrequencies

Function to explore read frequencies in targeted regions and out targeted regions.
plotGeneAttrPerFeat

Plot the attribute value for all the features of a selected gene.
summarizePanel

Function to summarize a featurePanel slot at a gene level.
initialize

TargetExperiment object constructor.
plotAttrPerform

Plot feature performance of a TargetExperiment object.