boxplot: Boxplot

In jmacdon/oligo: Preprocessing tools for oligonucleotide arrays

Description

Boxplot for observed (log-)intensities in a FeatureSet-like object (ExpressionFeatureSet, ExonFeatureSet, SnpFeatureSet, TilingFeatureSet) and ExpressionSet.

Usage

## 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, ...)

Arguments

x	a FeatureSet-like object or ExpressionSet object.
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.

Details

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').

Note

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.

See Also

hist, image, sample, set.seed

jmacdon/oligo documentation built on Aug. 11, 2020, 12:32 a.m.