Man pages for MAnorm2
Tools for Normalizing and Comparing ChIP-seq Samples
| 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 |
| distBioCond | Quantify the Distance between Each Pair of Samples in a... |
| estimateD0 | Workhorse Function for Estimating Number of Prior Degrees of... |
| estimateD0Robust | Estimate Number of Prior Degrees of Freedom in a Robust... |
| estimatePriorDf | Assess the Goodness of Fit of Mean-Variance Curves |
| estimatePriorDfRobust | Assess the Goodness of Fit of Mean-Variance Curves in a... |
| 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... |
| 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? |
| MAnorm2 | MAnorm2: a Package for Normalizing and Comparing ChIP-seq... |
| MA.pcc | Deduce Pearson Correlation Coefficient between M & A Values |
| MAplot | Generic MA Plotting |
| MAplot.bioCond | Create an MA Plot on Two 'bioCond' Objects |
| MAplot.diffBioCond | Create an MA Plot on Results of Comparing Two 'bioCond'... |
| meanVarLocalFit | Fit Mean-Variance Trend by Local Regression |
| mean_var_logwinf | Expectation and Variance of Log Winsorized _F_ Distribution |
| meanVarParaFit | Parametrically Fit a Mean-Variance Curve |
| 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 |
| plotMeanVarCurve | Plot a Mean-Variance Curve |
| plotMVC | Plot a Mean-Variance Curve on a Single 'bioCond' Object |
| plot.varTestBioCond | Plot a 'varTestBioCond' 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... |
| setPriorDfRobust | The Robust Counterpart of 'setPriorDf' |
| setPriorDfVarRatio | Set the Number of Prior Degrees of Freedom and Variance Ratio... |
| setWeight | Set the Weights of Signal Intensities Contained in a... |
| 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' |
