Man pages for genomaths/MethylIT.utils
MethylIT utility
| bootstrap2x2 | bootstrap2x2 |
| classPerform | Classification performance based on divergences of... |
| colorBar | Color bar for heatmaps |
| countSignal | Count the Sites Carrying an Arbitrary Signal Inside Genomic... |
| divTest | Group Comparisons of Information Divergences Based on... |
| dmpClustering | DMP Clustering |
| dmpDensity | Linear density of DMPs at a given genomic region |
| dot-colorBar | Color bar for heatmaps |
| evalDetection | Evaluate detection performance of a signal detector |
| evaluateModel | Evaluate a model using the Akaike information criterion (AIC) |
| findCutpoint | Find a cutoff of divergences of methylation level values |
| GeneUpDownStream | Get Genes plus Up and Down Stream Regions |
| getGRegionsStat | Statistic of Genomic Regions |
| getGRegionsStat2 | Statistic of Genomic Regions |
| getMethContext | Get Methylation Context from a chromosome DNA sequence |
| GRMatrix | Simulated matrix of arbitrary methylation signal used in the... |
| hclust_rect | Draw Rectangles with Background Colors Around Hierarchical... |
| heatmapChr | Heatmap of GRanges Object |
| jensenSDiv | Compute Jensen-Shannon Divergence |
| ksTest | Kolmogorov-Smirnov statistics |
| predict.ProbDistr | Predict function for probability distributions in Methyl-IT |
| propTest | Beta Regression for methylation levels and rates |
| rmstGR | Root Mean Square Test for Methylation Analysis |
| shannonEntr | Compute Shannon Entropy |
| signal2bins | Genomic Signal to Summarized Bins |
| signals2bins | Genomic Signals to Summarized Bins |
| simulateCounts | Simulate read counts of methylated and unmethylated cytosines |
| slidingGRanges | Generates intervals for a GRanges objects |
