iDEA.FDR: We constructed a permuted null distribution by permuting gene...

In xzhoulab/iDEA: Integrative Differential Expression and Gene Set Enrichment Analysis

We constructed a permuted null distribution by permuting gene labels. Specifically, we permuted the gene labels of annotation matrix to construced the null pvakue for gene sets. Then we calculate FDR for each gene sets given the permuted null distribution

Description

We constructed a permuted null distribution by permuting gene labels. Specifically, we permuted the gene labels of annotation matrix to construced the null pvakue for gene sets. Then we calculate FDR for each gene sets given the permuted null distribution

Usage

iDEA.FDR(object.alt, object.null, numPermute = 10)

Arguments

object.alt	iDEA object under the alternative. iDEA analysis in this object was performed using real gene sets
object.null	iDEA object under the permuted null. iDEA analysis in this object was performed by permuting the gene labels in gene sets.
numPermute	Number of permutation used in object.null. Default is 10.

Value

Returns a data frame which stores the results of iDEA with FDR values for each gene sets

xzhoulab/iDEA documentation built on Oct. 8, 2022, 8:54 a.m.