showOneDMR: Visualze the count data for one DMR

In haowulab/DSS: Dispersion shrinkage for sequencing data

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.

Author(s)

Hao Wu <[e-mail]>

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)

haowulab/DSS documentation built on Oct. 28, 2023, 6:59 p.m.