Man pages for MAnorm2
Tools for Normalizing and Comparing ChIP-seq Samples

aovBioCondPerform a Moderated Analysis of Variance on 'bioCond' Objects
bioCondCreate a 'bioCond' Object to Group ChIP-seq Samples
checkCountTableCheck the Regularity of a Count Table
checkIndexCheck the Validity of an Index Vector
cmbBioCondCombine a Set of 'bioCond' Objects into a Single 'bioCond'
diffTestGeneric Differential Test
distBioCondQuantify the Distance between Each Pair of Samples in a...
estimateD0Workhorse Function for Estimating Number of Prior Degrees of...
estimateD0RobustEstimate Number of Prior Degrees of Freedom in a Robust...
estimatePriorDfAssess the Goodness of Fit of Mean-Variance Curves
estimatePriorDfRobustAssess the Goodness of Fit of Mean-Variance Curves in a...
estimateSizeFactorsEstimate Size Factors of ChIP-seq Samples
estimateVarRatioEstimate Relative Variance Ratio Factors of 'bioCond' Objects
estParamHyperChIPThe Parameter Estimation Framework of HyperChIP
extendMeanVarCurveExtend the Application Scope of a Mean-Variance Curve
fitMeanVarCurveFit a Mean-Variance Curve
H3K27AcChIP-seq Samples for H3K27Ac in Human Lymphoblastoid Cell...
intervalMeansDeduce the Sample Mean Signal Intensity
intervalVarsSample Variance of Replicated Signal Intensities
inv.trigammaInversion of Trigamma Function
isSymPosDefIs a Real Matrix Symmetric and Positive Definite?
MAnorm2MAnorm2: a Package for Normalizing and Comparing ChIP-seq...
MA.pccDeduce Pearson Correlation Coefficient between M & A Values
MAplotGeneric MA Plotting
MAplot.bioCondCreate an MA Plot on Two 'bioCond' Objects
MAplot.diffBioCondCreate an MA Plot on Results of Comparing Two 'bioCond'...
meanVarLocalFitFit Mean-Variance Trend by Local Regression
mean_var_logwinfExpectation and Variance of Log Winsorized _F_ Distribution
meanVarParaFitParametrically Fit a Mean-Variance Curve
mvcID.newCreate a New Unique ID for a Mean-Variance Curve
normalizePerform MA Normalization on a Set of ChIP-seq Samples
normalizeBySizeFactorsNormalize ChIP-seq Samples by Their Size Factors
normBioCondPerform MA Normalization on a Set of 'bioCond' Objects
normBioCondBySizeFactorsNormalize 'bioCond' Objects by Their Size Factors
normCoefDeduce MA Normalization Coefficients
plot.aovBioCondPlot an 'aovBioCond' Object
plot.matrixVisualize a Matrix of Numeric Values
plotMeanVarCurvePlot a Mean-Variance Curve
plotMVCPlot a Mean-Variance Curve on a Single 'bioCond' Object
plot.varTestBioCondPlot a 'varTestBioCond' Object
print.bioCondPrint a 'bioCond' Object
print.summaryBioCondPrint a 'summaryBioCond' Object
scaleMeanVarCurveScale a Mean-Variance Curve
scaleMeanVarCurveRobustScale a Mean-Variance Curve in a Robust Manner
setMeanVarCurveSet the Mean-Variance Curve of a Set of 'bioCond' Objects
setPriorDfSet the Number of Prior Degrees of Freedom of Mean-Variance...
setPriorDfRobustThe Robust Counterpart of 'setPriorDf'
setPriorDfVarRatioSet the Number of Prior Degrees of Freedom and Variance Ratio...
setWeightSet the Weights of Signal Intensities Contained in a...
summary.bioCondSummarize a 'bioCond' Object
util.trigammaUtility Trigamma Function
varRatioCompare Variance Ratio Factors of Two 'bioCond' Objects
varTestBioCondCall Hypervariable and Invariant Intervals for a 'bioCond'
vstBioCondApply a Variance-Stabilizing Transformation to a 'bioCond'
MAnorm2 documentation built on Sept. 13, 2021, 5:06 p.m.