Man pages for ericaenjoy3/TdAvg
Tornado and Average Plots of Coverage Signals Centered on Peaks
| appendInfo-methods | append width and step size to an 'info' object |
| avgplot-methods | Plot average coverage signals stratified by clusters and by... |
| bplot-method | Plot a box plot |
| chip-class | An S4 class to represent bed file of chip-seq peaks. |
| chipConst-mehtods | construct an 'chip' object |
| clusterR-methods | Kmeans subclustering within each clusters of peaks |
| info-class | An S4 class to represent information of peaks to keep, to... |
| matlist-class | An S4 class to represent coverage value and ylab for plotting |
| matlistConst-methods | construct an 'matlist' object |
| mergeRep-methods | Merge within-group smaples' coverage signals |
| orderbyIntIdx-methods | orderbyIntIdx |
| orderClus-methods | order clusters in the 4th col of a bed file according to a... |
| outliers-methods | set currently kept peaks to be discarded if any NA coverage... |
| reord-methods | Reorder peaks (specified info.obj) by the descending order of... |
| returnIntIdx-methods | integer index (peak order) to keep of an 'info' object |
| rmSmallClus-methods | remove small (size<1000) clusters |
| subsetbyBoolIdx-methods | subset by boolean index |
| subsetbyIntIdx-methods | subset by integer index |
| tdplot-method | Plot a tornado plot |
| updateChip-methods | Update the 'bed' slot of the 'chip' object by the order and... |
| updateClus-methods | Update the label of peaks in 'bed' slot of an 'chip' object |
| updateMatlist-methods | Update the 'll' slot of the 'matlist' object by the order and... |
| writeChip-methods | Output the 'bed' slot of the 'chip' object to file. |
