Man pages for genomaths/MethylIT
Methylation Analysis Based on Signal Detection
| AICmodel | Akaike's Information Criterion (AIC) |
| AICquasiPoisson | AIC for Quasi-Poisson glm model |
| beta_bin_meth | Beta-binomial Posterior Methylation Levels |
| betaBinPosteriors | Beta binomial posteriors |
| BICmodel | Bayesian Information Criterion (BIC) |
| boltzman_factor | Boltzmann's Factors |
| coef | Extract Model Coefficients |
| countTest2 | Regression Test for Count |
| cutpoint | Cutpoint of the 'PS' simulated dataset used in the examples |
| dmpClusters | DMP clustering |
| dmps | Simulated dataset of DMPs used in examples |
| dmrfinder | Find Differentially Methylated Regions (DMRs) |
| ds | Simulated dataset of RangedGlmDataSet class object (DMPs... |
| estimateBayesianDivergence | Information divergence estimator |
| estimateBetaDist | Select the beta distribution that fit specified quantiles |
| estimateCutPoint | Estimate cutpoints to distinguish the treatment methylation... |
| estimateDivergence | Information Divergences of Methylation Levels |
| estimateECDF | A variant of Empirical Cumulative Distribution Function... |
| estimateGLM | Poisson and Negative Binomial regression analysis. |
| estimateHellingerDiv | Hellinger divergence of methylation levels |
| estimateJDiv | J Information Divergence of Methylation Levels |
| evaluateDIMPclass | Evaluate DMPs Classification |
| evaluateModel | Evaluate a model using the Akaike information criterion (AIC) |
| Extract | Subscript operator for objects from several Methyl-IT classes |
| filterByCoverage | Filter methylation counts by coverage |
| filterGRange | Filter methylation counts by coverage in a GRanges object |
| FisherTest | Fisher's exact test for read counts on GRanges objects |
| fitGammaDist | Nonlinear fit of Gamma CDF (Gamma) |
| fitGGammaDist | Nonlinear fit of Generalized Gamma CDF (GGamma) |
| fitLogNormDist | Nonlinear fit of Log-Normal CDF (LogNorm) |
| GeneUpDownStream | Get Genes plus Up and Down Stream Regions |
| getBaseMeansAndVariances | Calculate the means and variances by row |
| getDIMPatGenes | Count DMPs at gene-body |
| getDMGs | DMGs Estimation on Specified Genomic Region |
| getDMPatRegions | Count DMPs at Genomic Regions |
| getGEOSuppFiles | Get Supplemental Files from GEO |
| getGRangesStat | Statistic of Genomic Regions |
| getPotentialDIMP | Potential methylation signal |
| ggamma | Generalized Gamma distribution |
| gibb_entropy | Gibbs entropy of Generalized Gamma Distribution |
| glmDataSet | Data set constructor for class glmDataSet |
| gmMean | Calculate the geometric mean |
| gof | Simulated dataset of nonlinear fits used in the examples |
| gofReport | Report the Best Fitted Probability Distribution Model |
| gunzip | Decompress 'gzip' files |
| HD | Simulated dataset of Hellinger divergences used in the... |
| hdiv | Simulated dataset of Information divergences used in the... |
| helmholtz_free_energy | Helmholtz Free Energy of Generalized Gamma Distribution |
| lapply | Apply a function over a list-like object preserving its... |
| lda_perf | Classification LDA model for simulated dataset of DMPs used... |
| logit_perf | Classification logistic model for simulated dataset of DMPs... |
| machine_ent | Molecular Machine Entropy |
| meth_levels | Compute methylation levels |
| MethylIT | MethylIT: Methylation Analysis Based on Signal Detection and... |
| mlCutpoint | Machine-learning Approach for Cutpoint Estimation |
| nonlinearFitDist | Nonlinear fit of Information divergences distribution |
| pcaLDA | Linear Discriminant Analysis (LDA) using Principal Component... |
| pcaLda_perf | Classification PCA+LDA model for simulated dataset of DMPs... |
| pcaLogisticR | Logistic Classification Model using Principal Component... |
| pcalogit_perf | Classification logistic model for simulated dataset of DMPs... |
| pcaQDA | Quadratic Discriminant Analysis (QDA) using Principal... |
| pcaQda_perf | Classification PCA+QDA model for simulated dataset of DMPs... |
| pjob_split | Parallel Job Split |
| poolFromGRlist | Methylation pool from a list of GRanges objects with... |
| predict | Prediction Method of Random Forest for 'pDMP' Objects |
| predict.cdfMODEL | Predict function for probability distributions in Methyl-IT |
| predictDIMPclass | Predict DIMP class |
| predict.ldaDMP | Predict function for 'ldaDMP' method |
| predict.LogisticR | Predict function for logistic regression model from... |
| predict.qdaDMP | Predict function for 'qdaDMP' method |
| print.glmDataSet | Printing object from *_glmDataSet_* and... |
| print.mlDMP | Printing object from _ldaDMP_ and _qdaDMP_ classes by simple... |
| PS | Simulated dataset of potential DMPs used in examples |
| pweibull3P | Weibull distribution with three parameters |
| qda_perf | Classification LDA model for simulated dataset of DMPs used... |
| rcounts | Simulated dataset of read counts used in the examples |
| readCounts2GRangesList | Read files of methylation count tables |
| selectDIMP | Selection of DMPs |
| simpleCutPoint | Simple Cutpoint estimation |
| slidingGRegions | Generates intervals for a GRanges objects |
| sortBySeqnameAndStart | Sorting 'GRanges' objects |
| uniqueGRanges | Unique genomic ranges from a list of GRanges objects |
| uniqueGRfilterByCov | Unique 'GRanges-class' of methylation read counts filtered by... |
| unlist | Flatten lists extended to any class |
| validateClass | Function to validate S3 classes in MethylIT |
| weibull3P | Nonlinear fit of Weibull CDF |
