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Last data update: 2014.03.03

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Results 1 - 10 of 27 found.
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TarSeqQC-package (Package: TarSeqQC) : TarSeqQC: Targeted Sequencing Experiment Quality Control R package

The package models targeted sequencing experiment output using previous packages. This package includes the new following features:

● Data Source: BioConductor
● Keywords:
● Alias: TarSeqQC-package
● 0 images

biasExploration (Package: TarSeqQC) : Plot attribute density and boxplot for each bias source quartile.

biasExploration plots density and box-plot of the analyzed attribute for eaach bias source' quartiles. It helps the identification of some bias due to high source values, for example, high gc content. This graphics could plot together using the ggplot2 geom_violin method.

● Data Source: BioConductor
● Keywords:
● Alias: biasExploration, biasExploration,TargetExperiment-method, biasExploration-methods
● 1 images

buildFeaturePanel (Package: TarSeqQC) : Function to build a feature panel based on specific genomic regions.

buildFeaturePanel builds panel slots of a TargetExperiment object. Input can be a bam file or a pileup matrix. If the bed file contains a high number of amplicons, the bam file as input is recommended in order to diminish memory requirements. The resulting object is a GRanges instance having panel and counts/coverage information.

● Data Source: BioConductor
● Keywords:
● Alias: buildFeaturePanel, buildFeaturePanel,TargetExperiment-method, buildFeaturePanel-methods
● 0 images

addStatSummSheet (Package: TarSeqQC) : Build excel report of the Target Experiment.

addStatSummSheet adds the statistics summary sheet to the workbook that contains the Target Experiment Report.

● Data Source: BioConductor
● Keywords:
● Alias: addStatSummSheet, addStatSummSheet,TargetExperiment-method, addStatSummSheet-methods, buildReport, buildReport,TargetExperiment-method, buildReport-methods, ggplotColours, ggplotColours,TargetExperiment-method, ggplotColours-methods
● 0 images

TargetExperiment-class (Package: TarSeqQC) : TargetExperiment S4 class implementation in R

This S4 class represents a Targeted Sequencing Experiment in R. Targeted Sequencing Experiments are characterized by a 'bed file' that contains the specification of the explored 'features' as a 'panel'. This features could be amplicons, exons, transcripts, among others. In general each feature is associated to one gene. A gene could be related to many features. This class allows the representation and quality control of a Targeted Sequencing Experiment.

● Data Source: BioConductor
● Keywords:
● Alias: TargetExperiment-class
● 0 images

TargetExperiment (Package: TarSeqQC) : TargetExperiment constructor

TargetExperiment creates a TargetExperiment object with the architecture specified by the bed and alingment BAM files. If 'scanBamP' and/or 'pileupP' parameters are not specified, default values of their constructors will be used. attribute and feature parameters can be setted after constructor calling.

● Data Source: BioConductor
● Keywords:
● Alias: TargetExperiment, TargetExperiment-methods
● 0 images

getBedFile (Package: TarSeqQC) : Getters for TargetExperiment object.

Obtain TargetExperiment's slot information, according to the given function call.

● Data Source: BioConductor
● Keywords:
● Alias: getAttribute, getAttribute,TargetExperiment-method, getAttribute-methods, getBamFile, getBamFile,TargetExperiment-method, getBamFile-methods, getBedFile, getBedFile,TargetExperiment-method, getBedFile-methods, getFastaFile, getFastaFile,TargetExperiment-method, getFastaFile-methods, getFeature, getFeature,TargetExperiment-method, getFeature-methods, getFeaturePanel, getFeaturePanel,TargetExperiment-method, getFeaturePanel-methods, getGenePanel, getGenePanel,TargetExperiment-method, getGenePanel-methods, getLowCtsFeatures, getLowCtsFeatures,TargetExperiment-method, getLowCtsFeatures-methods, getPileupP, getPileupP,TargetExperiment-method, getPileupP-methods, getRegion, getRegion,TargetExperiment-method, getRegion-methods, getScanBamP, getScanBamP,TargetExperiment-method, getScanBamP-methods
● 0 images

initialize (Package: TarSeqQC) : TargetExperiment object constructor.

initialize creates the TargetExperiment object architecture for the specified bed and alingment BAM files. If 'scanBamP' and/or 'pileupP' parameters are not specified, default values of their constructors will be used.

● Data Source: BioConductor
● Keywords:
● Alias: initialize, initialize,TargetExperiment-method
● 0 images

plot (Package: TarSeqQC) : Plot TargetExperiment object overview.

plot allows a fast and simple representation of one feature panel using a polar histogram plot. Histogram bar reflects the percentage of features that have shown the analyzed attribute in a user setted interval. The resulting graph can be busy and might be better off saved.

● Data Source: BioConductor
● Keywords:
● Alias: plot, plot,TargetExperiment,ANY-method
● 1 images

plotAttrExpl (Package: TarSeqQC) : Plot attribute exploration of a TargetExperiment object.

plotAttrExpl plots density and box-plot of the analyzed attribute at a feature or gene level. This graphics could plot together using the ggplot2 geom_violin method.

● Data Source: BioConductor
● Keywords:
● Alias: plotAttrExpl, plotAttrExpl,TargetExperiment-method, plotAttrExpl-methods
● 1 images