plotMethMap {BiSeq} | R Documentation |
A heatmap like plot is generated showing the relative methylation of single CpG sites. Samples are clustered hierarchically.
plotMethMap(object, region, groups, intervals, ...)
object |
A |
region |
A |
groups |
OPTIONAL. A |
intervals |
OPTIONAL. A |
... |
Further arguments passed to the |
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.
Hans-Ulrich Klein
heatmap
, BSraw-class
, BSrel-class
, filterBySharedRegions
,
filterByCov
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)