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. |
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