Tools for Normalizing and Comparing ChIP-seq Samples

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Documentation for package ‘MAnorm2’ version 1.2.2

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

Help Pages

aovBioCond	Perform a Moderated Analysis of Variance on 'bioCond' Objects
bioCond	Create a 'bioCond' Object to Group ChIP-seq Samples
checkCountTable	Check the Regularity of a Count Table
checkIndex	Check the Validity of an Index Vector
cmbBioCond	Combine a Set of 'bioCond' Objects into a Single 'bioCond'
diffTest	Generic Differential Test
diffTest.bioCond	Generic Differential Test
distBioCond	Quantify the Distance between Each Pair of Samples in a 'bioCond'
estimateD0	Workhorse Function for Estimating Number of Prior Degrees of Freedom
estimateD0Robust	Estimate Number of Prior Degrees of Freedom in a Robust Manner
estimatePriorDf	Assess the Goodness of Fit of Mean-Variance Curves
estimatePriorDfRobust	Assess the Goodness of Fit of Mean-Variance Curves in a Robust Manner
estimateSizeFactors	Estimate Size Factors of ChIP-seq Samples
estimateVarRatio	Estimate Relative Variance Ratio Factors of 'bioCond' Objects
estParamHyperChIP	The Parameter Estimation Framework of HyperChIP
extendMeanVarCurve	Extend the Application Scope of a Mean-Variance Curve
fitMeanVarCurve	Fit a Mean-Variance Curve
H3K27Ac	ChIP-seq Samples for H3K27Ac in Human Lymphoblastoid Cell Lines
intervalMeans	Deduce the Sample Mean Signal Intensity
intervalVars	Sample Variance of Replicated Signal Intensities
inv.trigamma	Inversion of Trigamma Function
isSymPosDef	Is a Real Matrix Symmetric and Positive Definite?
MA.pcc	Deduce Pearson Correlation Coefficient between M & A Values
MAnorm2	MAnorm2: a Package for Normalizing and Comparing ChIP-seq Samples
MAplot	Generic MA Plotting
MAplot.bioCond	Create an MA Plot on Two 'bioCond' Objects
MAplot.default	Generic MA Plotting
MAplot.diffBioCond	Create an MA Plot on Results of Comparing Two 'bioCond' Objects
meanVarLocalFit	Fit Mean-Variance Trend by Local Regression
meanVarParaFit	Parametrically Fit a Mean-Variance Curve
mean_var_logwinf	Expectation and Variance of Log Winsorized _F_ Distribution
mvcID.new	Create a New Unique ID for a Mean-Variance Curve
normalize	Perform MA Normalization on a Set of ChIP-seq Samples
normalizeBySizeFactors	Normalize ChIP-seq Samples by Their Size Factors
normBioCond	Perform MA Normalization on a Set of 'bioCond' Objects
normBioCondBySizeFactors	Normalize 'bioCond' Objects by Their Size Factors
normCoef	Deduce MA Normalization Coefficients
plot.aovBioCond	Plot an 'aovBioCond' Object
plot.matrix	Visualize a Matrix of Numeric Values
plot.varTestBioCond	Plot a 'varTestBioCond' Object
plotMeanVarCurve	Plot a Mean-Variance Curve
plotMVC	Plot a Mean-Variance Curve on a Single 'bioCond' Object
print.bioCond	Print a 'bioCond' Object
print.summaryBioCond	Print a 'summaryBioCond' Object
scaleMeanVarCurve	Scale a Mean-Variance Curve
scaleMeanVarCurveRobust	Scale a Mean-Variance Curve in a Robust Manner
setMeanVarCurve	Set the Mean-Variance Curve of a Set of 'bioCond' Objects
setPriorDf	Set the Number of Prior Degrees of Freedom of Mean-Variance Curves
setPriorDfRobust	The Robust Counterpart of 'setPriorDf'
setPriorDfVarRatio	Set the Number of Prior Degrees of Freedom and Variance Ratio Factors
setWeight	Set the Weights of Signal Intensities Contained in a 'bioCond'
summary.bioCond	Summarize a 'bioCond' Object
util.trigamma	Utility Trigamma Function
varRatio	Compare Variance Ratio Factors of Two 'bioCond' Objects
varTestBioCond	Call Hypervariable and Invariant Intervals for a 'bioCond'
vstBioCond	Apply a Variance-Stabilizing Transformation to a 'bioCond'