get_fisher_info {KEGGlincs} | R Documentation

## Perform Fisher's Exact test for edges in pathway

### Description

Obtain a measure for strength and significance for the relationship (i.e. an edge) based on the concordance/discordance of UP-and-DOWN regulated genes shared by two different experimental gene-knockouts Intended for use within `overlap_info`

### Usage

    get_fisher_info(edges, method)

### Arguments

`edges` | The set of eges to be analyzed; Although the intended use is for LINCS data overlaps, the function should work with any typical data object as long as it has columns labeled ("UP", "DOWN", "UK1_DK2", "DK1_UK2") that contain integer values.
`method` | The method to correct/adjust p-values for multiple testing. For available methods, type 'p.adjust.methods' into command promt and press enter.

### Value

The input edge data.frame object with additional columns containing the results of the applied statistical test

### Examples

    ex.data <- data.frame("UP" = c(70,6), "DOWN" = c(8,20),
                        "UK1_DK2" = c(4,47), "DK1_UK2" = c(3, 28))

    overlaps <- get_fisher_info(ex.data, method = "BH")

[Package KEGGlincs version 1.8.0 Index]