MAplot {oligo} | R Documentation |
Create MA plots using a reference array (if one channel) or using channel2 as reference (if two channel).
MAplot(object, ...) ## S4 method for signature 'FeatureSet' MAplot(object, what=pm, transfo=log2, groups, refSamples, which, pch=".", summaryFun=rowMedians, plotFun=smoothScatter, main="vs pseudo-median reference chip", pairs=FALSE, ...) ## S4 method for signature 'TilingFeatureSet' MAplot(object, what=pm, transfo=log2, groups, refSamples, which, pch=".", summaryFun=rowMedians, plotFun=smoothScatter, main="vs pseudo-median reference chip", pairs=FALSE, ...) ## S4 method for signature 'PLMset' MAplot(object, what=coefs, transfo=identity, groups, refSamples, which, pch=".", summaryFun=rowMedians, plotFun=smoothScatter, main="vs pseudo-median reference chip", pairs=FALSE, ...) ## S4 method for signature 'matrix' MAplot(object, what=identity, transfo=identity, groups, refSamples, which, pch=".", summaryFun=rowMedians, plotFun=smoothScatter, main="vs pseudo-median reference chip", pairs=FALSE, ...) ## S4 method for signature 'ExpressionSet' MAplot(object, what=exprs, transfo=identity, groups, refSamples, which, pch=".", summaryFun=rowMedians, plotFun=smoothScatter, main="vs pseudo-median reference chip", pairs=FALSE, ...)
object |
|
what |
function to be applied on |
transfo |
function to transform the data prior to plotting. |
groups |
factor describing groups of samples that will be combined prior to plotting. If missing, MvA plots are done per sample. |
refSamples |
integers (indexing samples) to define which subjects
will be used to compute the reference set. If missing, a
pseudo-reference chip is estimated using |
which |
integer (indexing samples) describing which samples are to be plotted. |
pch |
same as |
summaryFun |
function that operates on a matrix and returns a vector that will be used to summarize data belonging to the same group (or reference) on the computation of grouped-stats. |
plotFun |
function to be used for plotting. Usually
|
main |
string to be used in title. |
pairs |
logical flag to determine if a matrix of MvA plots is to be generated |
... |
Other arguments to be passed downstream, like |
MAplot will take the following extra arguments:
subset
: indices of elements to be plotted to reduce
impact of plotting 100's thousands points (if pairs=FALSE only);
span
: see loess
;
family.loess
: see loess
;
addLoess
: logical flag (default TRUE) to add a loess
estimate;
parParams
: list of params to be passed to par() (if
pairs=TRUE only);
Plot
Benilton Carvalho - based on Ben Bolstad's original MAplot function.
if(require(oligoData) & require(pd.hg18.60mer.expr)){ data(nimbleExpressionFS) nimbleExpressionFS groups <- factor(rep(c('brain', 'UnivRef'), each=3)) data.frame(sampleNames(nimbleExpressionFS), groups) MAplot(nimbleExpressionFS, pairs=TRUE, ylim=c(-.5, .5), groups=groups) }