| qsea-package | QSEA: Quantitative sequencing enrichment analysis and visualization |
| addCNV | estimate CNV information and add to qseaSet object |
| addContrast | fit GLMs to reduced model and test for significance |
| addCoverage | Import sequencing data |
| addEnrichmentParameters | Enrichment analysis |
| addLibraryFactors | Estimate effective library size |
| addNewSamples | Extends an exisiting qseaSet by new samples |
| addOffset | Estimate background reads |
| addParameters-method | qseaGLM class and its methods |
| addParameters-method | qseaSet class and its methods |
| addPatternDensity | Infer sequence pattern density values and add to qseaSet object |
| addSeqPref | Add sequence preference to qseaSet object |
| createQseaSet | Prepares a qseaSet Object |
| fitNBglm | Fit GLM for each window |
| getChrNames | qseaSet class and its methods |
| getChrNames-method | qseaSet class and its methods |
| getCNV | qseaSet class and its methods |
| getCNV-method | qseaSet class and its methods |
| getCounts | qseaSet class and its methods |
| getCounts-method | qseaSet class and its methods |
| getExampleQseaSet | Simulation of MeDIP seq QSEA set |
| getLibSize | qseaSet class and its methods |
| getLibSize-method | qseaSet class and its methods |
| getNormFactors | qseaSet class and its methods |
| getNormFactors-method | qseaSet class and its methods |
| getOffset | qseaSet class and its methods |
| getOffset-method | qseaSet class and its methods |
| getParameters | qseaSet class and its methods |
| getParameters-method | qseaGLM class and its methods |
| getParameters-method | qseaSet class and its methods |
| getPCA | Principle Component Analysis (PCA) in QSea |
| getRegions | qseaSet class and its methods |
| getRegions-method | qseaSet class and its methods |
| getSampleGroups | qseaSet class and its methods |
| getSampleGroups-method | qseaSet class and its methods |
| getSampleNames | qseaSet class and its methods |
| getSampleNames-method | qseaGLM class and its methods |
| getSampleNames-method | qseaPCA class and its methods |
| getSampleNames-method | qseaSet class and its methods |
| getSampleTable | qseaSet class and its methods |
| getSampleTable-method | qseaSet class and its methods |
| getWindowSize | qseaSet class and its methods |
| getWindowSize-method | qseaSet class and its methods |
| getZygosity | qseaSet class and its methods |
| getZygosity-method | qseaSet class and its methods |
| hasCNV | qseaSet class and its methods |
| hasCNV-method | qseaSet class and its methods |
| isSignificant | Finds Significant Regions |
| makeTable | Create a Results Table |
| normMethod | Definition of normalization procedure |
| plotCNV | Plots a Heatmap-like Overview of the CNVs |
| plotCoverage | Plots a genome-browser-like image of a region |
| plotEnrichmentProfile | Plotting functions for enrichment profiles |
| plotEPmatrix | Plotting functions for enrichment profiles |
| plotPCA | Plots for Principle Component Analysis (PCA) in QSEA |
| plotPCA-method | Plots for Principle Component Analysis (PCA) in QSEA |
| plotPCAfactors | Plots for Principle Component Analysis (PCA) in QSEA |
| plotPCAfactors-method | Plots for Principle Component Analysis (PCA) in QSEA |
| QSEA | QSEA: Quantitative sequencing enrichment analysis and visualization |
| qsea | QSEA: Quantitative sequencing enrichment analysis and visualization |
| qseaGLM | qseaGLM class and its methods |
| qseaGLM-class | qseaGLM class and its methods |
| qseaPCA | qseaPCA class and its methods |
| qseaPCA-class | qseaPCA class and its methods |
| qseaSet | qseaSet class and its methods |
| qseaSet-class | qseaSet class and its methods |
| regionStats | Counts the Windows in Regions of Interest |
| setZygosity | qseaSet class and its methods |
| setZygosity-method | qseaSet class and its methods |
| show-method | qseaGLM class and its methods |
| show-method | qseaPCA class and its methods |
| show-method | qseaSet class and its methods |