get_fisher_info: Perform Fisher's Exact test for edges in pathway

In uc-bd2k/KEGGlincs: Visualize all edges within a KEGG pathway and overlay LINCS data [option]

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")

uc-bd2k/KEGGlincs documentation built on May 3, 2019, 2:13 p.m.