plotDMRs: Plot differentially methylated regions (DMRs) found using the...
In charm: Analysis of DNA methylation data from CHARM microarrays

Description Usage Arguments Details Author(s) See Also Examples

Plot differentially methylated regions (DMRs) from tiling microarray data that were identified using the dmrFind function.

plotDMRs(dmrs, Genome, cpg.islands, exposure, outfile, which_plot=1:50, which_lines=NULL, which_points=which_lines, ADD=3000, cols=c("black","blue","red","gray","brown","pink","orange"), legend.size=1, smoo="loess", SPAN=300, DELTA=36, point.info=FALSE, pch.groups=NULL, panel3="pvalues", G=NULL, seq=NULL)

`dmrs`	a list object as returned by dmrFind.
`Genome`	the BSgenome object for the organism based upon which your array was designed.
`cpg.islands`	a table with columns "chr","start", and "end" for CpG islands to plot in the second panel.
`exposure`	The covariate of interest.
`outfile`	the name of the file to save (including the full path)
`which_plot`	numeric vector of indices identifying which DMR candidates from dmrs$dmrs to plot.
`which_lines`	vector specifying which groups (unique elements of exposure) to plot the lines for. If NULL (the default), plots lines for all groups. Only applies if exposure is categorical.
`which_points`	vector specifying which groups (unique elements of exposure) to plot the points for. If NULL (the default), plots points for all groups. Only applies if exposure is categorical.
`SPAN`	see DELTA. Only used if smoo="loess"
`DELTA`	span parameter in loess smoothing will = SPAN/(DELTA * number of probes in the plotted region). Only used if smoo="loess".
`smoo`	"loess" for loess smoother or "runmed" for running median smoother (runmed with k=3). This does not need to be the same as the smoo argument to dmrFind.
`ADD`	Number of base pairs to plot on either side of each DMR candidate (if it is covered on the array).
`cols`	vector of colors to use, one for each group (if covariate is categorical)
`point.info`	if TRUE, function returns a table identifying which sample is plotted with which number or letter (if pch.groups=NULL, the default).
`legend.size`	magnification factor for the legend
`pch.groups`	vector whose length is equal to the number of samples. Each unique value will be plotted with a different point type.
`panel3`	if panel3="G", the third panel of each DMR plot will show the difference between the median green channel value (after subtracting probe medians and correcting for gc content) between the 2 groups (i.e., the group defined by mod[,coef] in dmrFind minus the reference group). If panel="G", seq argument must be provided. If panel!="G", the 3rd panel will show -log10(dmrs$pval). G
`G`	matrix of green channel intensities to use for plotting in the 3rd panel if panel3="G".
`seq`	vector of probe sequences corresponding to the rows of G (and dmrs$cleanp) if panel3="G".