showOneDMR {DSS} | R Documentation |
Given one DMR and an BSseq object, this function generate a multiple panel figure, each for a sample, to visualze the counts. There is a bar at each CpG, the gray bar shows the total coverage, and the black bar shows the methylated count.
showOneDMR(OneDMR, BSobj, ext = 500, ylim)
OneDMR |
A data frame with one row representing one DMR. It must have chr, start, and end columns. This is typically a row from the result generated from callDMR. |
BSobj |
An object of class BSseq. |
ext |
The amount (in bps) the plotting region should be extended in both directions. |
ylim |
Y-axis limit. |
This function only generates a figure and has no return values.
Hao Wu <hao.wu@emory.edu>
callDMR
## Not run: require(bsseq) require(bsseqData) data(BS.cancer.ex) ## takea small portion of data and test BSobj <- BS.cancer.ex[140000:150000,] dmlTest <- DMLtest(BSobj, group1=c("C1", "C2", "C3"), group2=c("N1","N2","N3"), smoothing=TRUE, smoothing.span=500) ## call DMR based on test results dmrs <- callDMR(dmlTest) ## visualize one DMR showOneDMR(dmrs[1,], BSobj) ## End(Not run)