Package 'charm' - Bioconductor
Package 'charm' - Bioconductor
Package 'charm' - Bioconductor
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16 dmrPlot<br />
Author(s)<br />
Martin Aryee , Peter Murakami, Rafael Irizarry<br />
See Also<br />
dmrFind, readCharm, methp, dmrFdr<br />
Examples<br />
# See dmrFdr<br />
dmrPlot<br />
Plot differentially methylated regions (DMRs) found using the dmrFinder<br />
function.<br />
Description<br />
Usage<br />
Plot differentially methylated regions (DMRs) from tiling microarray data that were identified using<br />
the dmrFinder function. To plot DMRs identified using the dmrFind function, use the plotDMRs<br />
function.<br />
dmrPlot(dmr, which.table=1:length(dmr$tabs), which.plot=1:30, legend.size=1, all.lines=TRUE, all.poin<br />
Arguments<br />
dmr<br />
which.table<br />
which.plot<br />
legend.size<br />
all.lines<br />
all.points<br />
colors.l<br />
colors.p<br />
outpath<br />
cpg.islands<br />
Genome<br />
a list object as returned by dmrFinder.<br />
a vector of indices identifying which tables in the dmr list to plot regions from.<br />
a vector of indices identifying which regions (rows) from each table to plot.<br />
cex argument for the legend (factor by which to magnify/shrink the legend).<br />
if TRUE, plot the smooth lines for all groups. If FALSE, only for the 2 groups<br />
being compared.<br />
if TRUE, plot the points for all groups. If FALSE, only for the 2 groups being<br />
compared.<br />
a vector of line colors, one color for each group whose line is to be plotted (in<br />
alphabetical order).<br />
a vector of point colors, one color for each group whose points are to be plotted<br />
(in alphabetical order).<br />
where to save the output pdf file.<br />
a table with columns "chr","start", and "end" for CpG islands to plot in the<br />
second panel.<br />
the BSgenome object for the organism based upon which your array was designed.
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