geva.summarize {geva} | R Documentation

## Summarizes the GEVAInput

### Description

Performs the summarization step by calculating the central points and variation estimates of logFC values from the input data.

### Usage

    geva.summarize(
      ginput,
      summary.method = options.summary,
      variation.method = options.variation,
      ...
    )

    options.summary
    # c("mean", "median")

    options.variation
    # c("sd", "var", "mad")

### Arguments

`ginput` | a `GEVAInput` object
`summary.method` | single `character`, method used to calculate the central (summarized) logFC values
`variation.method` | single `character`, method used to calculate the distribution degree (variation) of the logFC values
`...` | additional arguments. Accepts `verbose` (`logical`, default is `TRUE`) to enable or disable printing the current progress

### Details

The `options.summary` refer to the available operations to calculate central logFC values (`mean` or `median`), whereas `options.variation` presents three functions to calculate logFC variation (`sd`: Standard Deviation; `var`: Variance; and `mad`: Median Absolute Deviation). Moreover, all those operations include a weighted counterpart applied using the `weights` table from the `GEVAInput` object.

### Value

A `GEVASummary` object

### See Also

`base::mean()`, `stats::median()`

`stats::var()`, `stats::sd()`, `stats::mad()`

### Examples

    ## Summarization of a randomly generated input
    ginput <- geva.ideal.example()     # Generates a random input example
    gsummary <- geva.summarize(ginput) # Summarizes with the default parameters
    plot(gsummary)                     # Plots the summarized data

[Package geva version 1.2.0 Index]