Man pages for ericaenjoy3/TdAvg
Tornado and Average Plots of Coverage Signals Centered on Peaks

appendInfo-methodsappend width and step size to an 'info' object
avgplot-methodsPlot average coverage signals stratified by clusters and by...
bplot-methodPlot a box plot
chip-classAn S4 class to represent bed file of chip-seq peaks.
chipConst-mehtodsconstruct an 'chip' object
clusterR-methodsKmeans subclustering within each clusters of peaks
info-classAn S4 class to represent information of peaks to keep, to...
matlist-classAn S4 class to represent coverage value and ylab for plotting
matlistConst-methodsconstruct an 'matlist' object
mergeRep-methodsMerge within-group smaples' coverage signals
orderClus-methodsorder clusters in the 4th col of a bed file according to a...
outliers-methodsset currently kept peaks to be discarded if any NA coverage...
reord-methodsReorder peaks (specified info.obj) by the descending order of...
returnIntIdx-methodsinteger index (peak order) to keep of an 'info' object
rmSmallClus-methodsremove small (size<1000) clusters
subsetbyBoolIdx-methodssubset by boolean index
subsetbyIntIdx-methodssubset by integer index
tdplot-methodPlot a tornado plot
updateChip-methodsUpdate the 'bed' slot of the 'chip' object by the order and...
updateClus-methodsUpdate the label of peaks in 'bed' slot of an 'chip' object
updateMatlist-methodsUpdate the 'll' slot of the 'matlist' object by the order and...
writeChip-methodsOutput the 'bed' slot of the 'chip' object to file.
ericaenjoy3/TdAvg documentation built on May 13, 2018, 8:33 p.m.