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' |