Usage
plotRegions(thetable, cleanp, chr, pos, seq=NULL, Genome, cpg.islands, exposure, exposure.continuous=FALSE, outfile="./myregions.pdf", which_lines=NULL, which_points=which_lines, ADD=3000, cols=c("black","red","blue","gray","green","orange","brown"), legend.size=1, smoo="loess", SPAN=300, DELTA=36, panel3="none", G=NULL, grs=NULL)
Arguments
thetable
a table with columns for "chr","start", and "end", identifying the genomic regions to plot (if they are covered on the array).
cleanp
the matrix of percent methylation estimates to be used for plotting
chr
vector of chromosome labels for the probes in cleanp
pos
vector of chromosomal coordinates for the probes in cleanp
seq
vector of probe sequences corresponding to the rows of G (and cleanp). Needed only if panel3="G".
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.
outfile
the name of the file to save (including the full path)
exposure
The covariate of interest.
exposure.continuous
set to TRUE if exposure is a continuous variable.
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.
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)
legend.size
magnification factor for the legend
smoo
"loess" for loess smoother or "runmed" for running median smoother (runmed with k=3).
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".
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
matrix of green channel intensities to use for plotting in the 3rd panel if panel3="G".
grs
if panel3="G", plot difference between the median green channel value (after subtracting probe medians and correcting for gc content) between these 2 groups.