summary.fdr.result {OCplus} | R Documentation

## Display functions for local fdr output

### Description

Display functions for output from `fdr1d` and `fdr2d`, summarizing the output, displaying the proportion of non-differentially expressed genes and extracting the list of top-regulated genes.

### Usage

    ## S3 method for class 'fdr.result'
    summary(object, ...)

    p0(x, how = FALSE)

    topDE(x, co = 0.1)

### Arguments

`x, object` | an object of class `fdr.result` created by `fdr1d` or `fdr2d`.
`how` | a logical value indicating whether to return only the numerical value of the proportion of non-differentially expressed genes, or a list whose second element indicates whether the proportion was estimated from the data or supplied by the user.
`...` | extra arguments, currently unused
`co` | cutoff for either FDR or fdr

### Value

For `summary.fdr.result`, a list with the summary items.

For `p0`, either a numerical value or a list with two elements, depending on the value of parameter `how`.

For `topDE`, the genes that have FDR (`EOC`) or fdr (`fdr1d`, `fdr2d`) less or equal than `co`, sorted by FDR or fdr respectively.

### Author(s)

A. Ploner

### See Also

`fdr1d`, `fdr2d`, `EOC`

### Examples

    # Create object res1d
    example(fdr1d)

    summary(res1d)
    p0(res1d)
    p0(res1d, how=TRUE)
    topDE(res1d)

[Package OCplus version 1.62.0 Index]