# Tools for Normalizing and Comparing ChIP-seq Samples

## Documentation for package ‘MAnorm2’ version 1.2.2

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

## 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'