hist

0th

Percentile

Density estimate

Plot the density estimates for each sample

Keywords
methods, hplot
Usage
## S3 method for class 'FeatureSet':
hist(x, transfo=log2, which=c("pm", "mm", "bg", "both", "all"),
                   nsample=10000, ...)

## S3 method for class 'ExpressionSet': hist(x, transfo=identity, nsample=10000, ...)

Arguments
x
FeatureSet or ExpressionSet object
transfo
a function to transform the data before plotting. See 'Details'.
nsample
number of units to sample and build the plot.
which
set of probes to be plotted ("pm", "mm", "bg", "both", "all").
...
arguments to be passed to matplot
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 hist methods for FeatureSet and Expression use a sample (via sample) of the probes/probesets to produce the plot (unless nsample > nrow(x)). Therefore, the user interested in reproducibility is advised to use set.seed.

Aliases
  • hist
  • hist-methods
  • hist,FeatureSet-method
  • hist,ExpressionSet-method
Documentation reproduced from package oligo, version 1.36.1, License: LGPL (>= 2)

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