mboxplot-methods {xps} | R Documentation |
Produce boxplots of relative M values for the set of arrays.
Usage
mboxplot(x, which = "", size = 0, transfo = log2, method = "mean", range = 0, ylim = c(-1,1), outline = FALSE, names = "namepart", ...)
x |
object of class DataTreeSet or ExprTreeSet . |
which |
type of probes to be used, for details see validData . |
size |
length of sequence to be generated as subset. |
transfo |
a valid function to transform the data, usually “log2”, or “0”. |
method |
method to create the reference data, “mean” or “median”. |
range |
determines how far the plot whiskers extend out from the box. |
ylim |
range for the plotted y values. |
outline |
if outline is not true, the outliers are not drawn. |
names |
optional vector of sample names. |
... |
optional arguments to be passed to boxplot . |
Create boxplots of M plots, where M is determined relative to a pseudo-mean reference chip.
For names=NULL
full column names of slot data
will be displayed while for
names="namepart"
column names will be displayed without name extension. If names
is a vector of column names, only these columns will displayed as boxplot.
For a DataTreeSet
object, data must first be attached using method
attachInten
.
Christian Stratowa
# load existing ROOT scheme file and ROOT data file scheme.test3 <- root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/")) data.test3 <- root.data(scheme.test3, paste(.path.package("xps"),"rootdata/DataTest3_cel.root",sep="/")) # need to attach scheme mask and probe intensities data.test3 <- attachMask(data.test3) data.test3 <- attachInten(data.test3) if (interactive()) { mboxplot(data.test3, ylim=c(-6,6)) } # optionally remove mask and data to free memory data.test3 <- removeInten(data.test3) data.test3 <- removeMask(data.test3)