Generates MA and scatter plots of differential binding analysis results.
1 2 3 4 5 6 
DBA 
DBA object, on which 
contrast 
number of contrast to report on. See 
method 
method or vector of methods to plot results for:

th 
significance threshold; all sites with FDR (or pvalues, see 
bUsePval 
logical indicating whether to use FDR (FALSE) or pvalue (TRUE) for thresholding. 
fold 
will only include sites with fold change greater than this as significant (colored red). 
bNormalized 
logical indicating whether to plot normalized data using normalization factors computed by differential analysis method (TRUE) or raw read counts (FALSE). 
factor 
string to be prepended to plot main title; e.g. factor name. 
bFlip 
logical indicating that order of groups in contrast should be "flipped", allowing control of which sample group will have positive and which will have negative fold changes. 
bXY 
logical indicating whether to draw MA plot (FALSE) or XY scatter plot (TRUE). 
dotSize 
size of points on plot (cex). 
bSignificant 
Logical indicating if points corresponding to significantly differentially bound sites
(based on 
bSmooth 
logical indicating that basic plot should be plotted using 
xrange 
vector of length 2 containing the desired minimum and maximum concentrations to plot. 
yrange 
vector of length 2 containing the desired minimum and maximum fold changes to plot. 
... 
passed to plot. 
Rory Stark
dba.analyze
1 2 3 4 5 6 7 8 9  data(tamoxifen_analysis)
# default MA plot
dba.plotMA(tamoxifen)
#XY plots (with raw and normalized data)
par(mfrow=c(1,2))
dba.plotMA(tamoxifen,bXY=TRUE,bSmooth=FALSE,bNormalized=FALSE)
dba.plotMA(tamoxifen,bXY=TRUE,bSmooth=FALSE,bNormalized=TRUE)

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