hist {oligo} | R Documentation

## Density estimate

### Description

Plot the density estimates for each sample

### Usage

    ## S4 method for signature 'FeatureSet'
    hist(x, transfo=log2, which=c("pm", "mm", "bg", "both", "all"),
                       nsample=10000, ...)

    ## S4 method for signature '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`.

[Package oligo version 1.51.2 Index]