Man pages for chroGPS
chroGPS2: Generation, visualization and differential analysis of epigenome maps
| addVar | Plot vector of a quantitative variable over a MDS map. |
| adjustPeaks | Adjust peak width so that samples obtained under different... |
| bg3 | Sample binding site and related data from BG3 cell line in... |
| boostMDS | Improve goodness-of-fit of a given MDS solution in terms of... |
| clusGPS | Computation of cluster density estimates for cluster contour... |
| clusGPS-class | Class '"clusGPS"' |
| combineGenesMatrix | Combine two datasets with epigenetic factor profiles at gene... |
| diffFactors | Performs differential analysis of chroGPS-factors maps based... |
| diffGenes | Performs differential analysis of chroGPS-genes maps based on... |
| distGPS | Compute matrix with pairwise distances between objects.... |
| distGPS-class | Class '"distGPS"' |
| domainDist | Overview of intra and inter-domain distances. |
| geneSetGPS | Highlight point (gene) position over a Multi-dimensional... |
| getURL | Retrieve file from URL. |
| gff2RDList | Retrieve binding site information from GFF3 files. |
| gps2xgmml | Export an 'mds' object to Cytoscape .xgmml format |
| mds | Metric and non-metric Multidimensional Scaling for a distGPS... |
| mds-class | Class '"mds"' |
| mergeClusters | Unsupervised cluster merging based on their observed overlap... |
| mergeReplicates | Merges information from epigenetic replicates at factor, gene... |
| procrustesAdj | Use Procrustes to adjust an MDS map containing samples... |
| profileClusters | Assess epigenetic profiles for genes present in each cluster... |
| rankFactorsbyDomain | Function to help selecting candidate epigenetic factors based... |
| rankFactorsbyProfile | Function to help selecting candidate epigenetic factors based... |
| s2 | Sample binding site and related data from S2 and BG3 cell... |
| splitDistGPS-class | Class '"splitDistGPS"' |
