Man pages for benja0x40/MRA.TA
Multi Resolution Analysis of Tiling Arrays
| backgroundBiasCorrection | Background bias correction |
| backgroundBiasEstimation | Background bias estimation |
| calc.Qi | Rank based scores |
| colorstrip | colorstrip |
| combineByFragment | Combine probe measurements by restriction fragments |
| computeRestrictionMap | Compute a restriction map |
| countProbesPerFragment | Count the number of accepted probes per restriction fragment |
| domainogram | Domainogram visualization |
| enrichmentQuality | Best and worst enrichment levels |
| enrichmentScore | Log-transformed enrichment scores |
| _hidden_/kdtree | [RESERVED] - Not Documented |
| _hidden_/kdtree.getDN | [RESERVED] - Not Documented |
| _hidden_/line.ends | [RESERVED] - Not Documented |
| _hidden_/localopt.c | [RESERVED] - Not Documented |
| _hidden_/mean.shift | [RESERVED] - Not Documented |
| _hidden_/new.domain.plot | [RESERVED] - Not Documented |
| _hidden_/plot.kdtree.border | [RESERVED] - Not Documented |
| _hidden_/rotate | [RESERVED] - Not Documented |
| kdtree | kd-tree representation of (A,M) values |
| kdtree.getDN | Neighbor selection |
| localopt.c | local optimization |
| lowessCorrection | LOWESS based normalization |
| makeColors | Represent numerical values by a color vector |
| matchFragmentsToProbes | Match restriction fragments to microarray probes |
| matchProbesToFragments | Match micro array probes to restriction fragments |
| mean.shift | Meanshift |
| new.domain.plot | Create a new multi-resolution plot |
| normalizeArrayData | Normalize tiling array data |
| plotDomains | Plot multi-resolution segmentation results |
| plot.kdtree.border | visualize the kd-tree structure |
| plotOptimalSegments | Plot multi-resolution segmentation results |
| plotProbeDistanceControls | Plot 4C enrichment versus distance to restriction sites |
| plotSelectedProbes | Plot 4C enrichment versus distance to restriction sites |
| processArgs | Extract command line arguments |
| readData | Read tabulated text files |
| segmentation | Multi-resolution segmentation |
| verifyInputFiles | Check input files |
| visualizationCoordinates | Continuous coordinates for domainogram visualization (x axis) |
| wSize2yAxis | Continuous coordinates for domainogram visualization (y axis) |
