Man pages for MatthiasLienhard/qsea
IP-seq data analysis and vizualization
| 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 |
| addPatternDensity | Infer sequence pattern density values and add to qseaSet... |
| addSeqPref | Add sequence preference to qseaSet object |
| createQseaSet | Prepares a qseaSet Object |
| example | Simulation of MeDIP seq QSEA set |
| fitNBglm | Fit GLM for each window |
| getPCA | Principle Component Analysis (PCA) in QSea |
| 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 |
| plotPCA | Plots for Principle Component Analysis (PCA) in QSEA |
| qseaGLM-class | qseaGLM class and its methods |
| qsea-package | QSEA: Quantitative sequencing enrichment analysis and... |
| qseaPCA-class | qseaPCA class and its methods |
| qseaSet-class | qseaSet class and its methods |
| regionStats | Counts the Windows in Regions of Interest |
