getDGETable: Extract table of differential results from 'K2' object

In montilab/K2Taxonomer: Creating annotated submodules of high-throughput data through recursive partitioning

Extract table of differential results from 'K2' object

Description

Create table differential analysis results from 'K2' object.

Usage

getDGETable(K2res)

Arguments

K2res

An object of class K2.

Value

A data.frame object with the following columns:

• gene: The gene ids from the 'ExpressionSet' object

• coef: The difference between the means of each subgroup at a given partition

• mean: The mean across all observations at the given partition

• t: The test statistic estimated by the 'limma' R package

• pval: The p-value estimated by the 'limma' R package

• fdr: The multiple hypothesis corrected fdr p-value, adjusted across all partitions

• B: The B-statistic estimated by the 'limma' R package

• edge: Indication of which subgroup the gene was assigned at a given partition

• node: The identifier of the partition

• direction: The direction of coefficient for the assigned gene

References

\insertRef

reed_2020K2Taxonomer \insertReflimmaK2Taxonomer \insertRefbhK2Taxonomer

Examples

## Read in ExpressionSet object
library(Biobase)
data(sample.ExpressionSet)

## Pre-process and create K2 object
K2res <- K2preproc(sample.ExpressionSet)

## Run K2 Taxonomer algorithm
K2res <- K2tax(K2res,
            stabThresh=0.5)

## Run differential analysis on each partition
K2res <- runDGEmods(K2res)

## Extract table of differential results
head(getDGETable(K2res))

montilab/K2Taxonomer documentation built on Jan. 25, 2024, 4:29 p.m.