IP-seq data analysis and vizualization


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Documentation for package ‘qsea’ version 1.6.0

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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