DSS (version 2.12.0)

showOneDMR: Visualze the count data for one DMR

Description

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.

Usage

showOneDMR(OneDMR, BSobj, ext = 500, ylim)

Arguments

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.

Value

This function only generates a figure and has no return values.

See Also

callDMR

Examples

## 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)