BiSeq (version 1.12.0)

plotMethMap: Plots methylation values of multiple samples in a given region

Description

A heatmap like plot is generated showing the relative methylation of single CpG sites. Samples are clustered hierarchically.

Usage

plotMethMap(object, region, groups, intervals, ...)

Arguments

object

A BSraw or BSrel object storing the methylation values.

region

A GRanges object giving the region of interest.

groups

OPTIONAL. A factor that will be encoded by a color bar.

intervals

OPTIONAL. A logical indicating whether neighboured CpG sites should be placed side by side (if FALSE) or whether the intervals between CpG sites should be preserved (if TRUE).

...

Further arguments passed to the heatmap function.

Details

The relative methylation values are passed to the heatmap function. Default colors are green (not methylated), black and red (methylated). To ensure that a relative methylation of 0 corresponds to green, 0.5 to black and 1 to red, the default value for the zlim argument of the heatmap function is set to c(0,1). And the default for the scale parameter is set to "none". If argument intervals is set to TRUE, region should not be too large (< 1kb) and respect the resolution of your screen.

See Also

heatmap, BSraw-class, BSrel-class, filterBySharedRegions, filterByCov

Examples

data(rrbs)
data(predictedMeth)
data(DMRs)

plotMethMap(rrbs, region = DMRs[4], groups = colData(rrbs)[, "group"])

plotMethMap(predictedMeth, region = DMRs[4],
            groups = colData(rrbs)[,"group"], intervals = FALSE)