densityPlots {iCheck} | R Documentation |
Draw estimated density plots for all arrays.
densityPlots( es, requireLog2 = TRUE, myxlab = "expression level", mymain = "density plots", datExtrFunc = exprs, fileFlag = FALSE, fileFormat = "ps", fileName = "densityPlots.ps")
es |
An |
requireLog2 |
logic. indicating if log2 transformation is required before estimating densities. |
myxlab |
character. indicating x-axis label. |
mymain |
character. indicating title of the plot. |
datExtrFunc |
name of the function to extract genomic data. For
an |
fileFlag |
logic. indicating if plot should be saved to an external figure file. |
fileFormat |
character. indicating the figure file type. Possible values are “ps”, “pdf”, or “jpeg”. All other values will produce “png” file. |
fileName |
character. indicating figure file name (file extension should be specified). For example,
you set |
A list object, the i-th element is the object returned by
function density
for the i-th array.
Weiliang Qiu <stwxq@channing.harvard.edu>, Brandon Guo <brandowonder@gmail.com>, Christopher Anderson <christopheranderson84@gmail.com>, Barbara Klanderman <BKLANDERMAN@partners.org>, Vincent Carey <stvjc@channing.harvard.edu>, Benjamin Raby <rebar@channing.harvard.edu>
# generate simulated data set from conditional normal distribution set.seed(1234567) es.sim = genSimData.BayesNormal(nCpGs = 100, nCases = 20, nControls = 20, mu.n = -2, mu.c = 2, d0 = 20, s02 = 0.64, s02.c = 1.5, testPara = "var", outlierFlag = FALSE, eps = 1.0e-3, applier = lapply) print(es.sim) densityPlots( es = es.sim, requireLog2 = FALSE, myxlab = "expression level", mymain = "density plots", datExtrFunc = exprs, fileFlag = FALSE, fileFormat = "ps", fileName = "densityPlots.ps")