# IP-seq data analysis and vizualization

## Documentation for package ‘qsea’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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