getDGEInter: Create interactive table of differential gene expression...

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

Create interactive table of differential gene expression analysis results from 'K2' object

Description

Create interactive table differential gene expression analysis results from 'K2' object.

Usage

getDGEInter(
  K2res,
  maxFDR = 0.05,
  minDiff = NULL,
  maxPval = NULL,
  genes = NULL,
  nodes = NULL,
  pagelength = 50
)

Arguments

K2res	A K2 class object.
maxFDR	Numeric. A value between 0 and 1 indicating the FDR cutoff for differential gene expressio analysis.
minDiff	Numeric. A value between 0 and 1 indicating the mean difference cutoff for differential gene expressio analysis.
maxPval	Numeric. A value between 0 and 1 indicating the p-value cutoff for differential gene expression analysis.
genes	Character. A vector of gene identifiers to display.
nodes	Character. A vector of node identifiers to display.
pagelength	Numeric. Number of rows to display in each page of output.

Value

An interactive data frame with the following columns:

• Gene: The identifier of the gene

• Node: The identifier of the partition

• Edge: The identifier of partition subgroup

• Direction: The direction of coefficient for the assigned gene

• P Value: The p-value estimated by differential analysis

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

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

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

References

\insertRef

reed_2020K2Taxonomer \insertReflimmaK2Taxonomer \insertRefbhK2Taxonomer

montilab/K2Taxonomer documentation built on April 5, 2025, 3:58 a.m.