boxplot {oligo} | R Documentation |
Boxplot for observed (log-)intensities in a FeatureSet-like object (ExpressionFeatureSet, ExonFeatureSet, SnpFeatureSet, TilingFeatureSet) and ExpressionSet.
## S4 method for signature 'FeatureSet' boxplot(x, which=c("pm", "mm", "bg", "both", "all"), transfo=log2, nsample=10000, target = "mps1", ...) ## S4 method for signature 'ExpressionSet' boxplot(x, which, transfo=identity, nsample=10000, ...)
x |
a |
which |
character defining what probe types are to be used in the plot. |
transfo |
a function to transform the data before plotting. See 'Details'. |
nsample |
number of units to sample and build the plot. |
... |
arguments to be passed to the default boxplot method. |
The 'transfo' argument will set the transformation to be used. For raw data, 'transfo=log2' is a common practice. For summarized data (which are often in log2-scale), no transformation is needed (therefore 'transfo=identity').
The boxplot methods for FeatureSet
and Expression
use a
sample (via sample
) of the probes/probesets to produce the
plot. Therefore, the user interested in reproducibility is advised to
use set.seed
.