Man pages for gamerino/TarSeqQC
TARgeted SEQuencing Experiment Quality Control
| 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... |
