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 |
addOffset | Estimate background reads |
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 |