showOneDMR {DSS} | R Documentation

## 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 <hao.wu@emory.edu>

### 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)

[Package DSS version 2.40.0 Index]