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.
|Author||Gabriela A. Merino, Cristobal Fresno, Yanina Murua, Andrea S. Llera and Elmer A. Fernandez|
|Date of publication||None|
|Maintainer||Gabriela Merino <email@example.com>|
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...