GeneScan3DKnock: GeneScan3DKnock: Knockoff-enhanced gene-based test for causal...

In Iuliana-Ionita-Laza/GeneScan3DKnock: Powerful gene-based testing by integrating long-range chromatin interactions and knockoff genotypes

GeneScan3DKnock: Knockoff-enhanced gene-based test for causal gene discovery (knockoff filter).

Description

This function performs the knockoff filter, and computes the q-value for each gene. This function takes the results from the GeneScan3D.KnockoffGeneration() function and get knockoff statistics and q-values.

Usage

GeneScan3DKnock(
  M = 5,
  p0 = GeneScan3DKnock.example$GeneScan3D.original,
  p_ko = cbind(GeneScan3DKnock.example$GeneScan3D.ko1,
    GeneScan3DKnock.example$GeneScan3D.ko2, GeneScan3DKnock.example$GeneScan3D.ko3,
    GeneScan3DKnock.example$GeneScan3D.ko4, GeneScan3DKnock.example$GeneScan3D.ko5),
  fdr = 0.1,
  gene_id = GeneScan3DKnock.example$gene.id
)

Arguments

M	Number of multiple knockoffs.
p0	A N-dimensional vector of the original GeneScan3D p-values, calculated using GeneScan3D.KnockoffGeneration() function.
p_ko	A N*M matrix of M knockoff GeneScan3D p-values, calculated using GeneScan3D.KnockoffGeneration() function.
fdr	The false discovery rate (FDR) threshold. The default is 0.1.
gene_id	The genes id for N genes considered in the analysis. Usually we consider N=~20,000 protein-coding genes.

Value

W	The knockoff statistics for each gene.
W.threshold	Threshold of W statistics. A gene is significant under GeneScan3DKnock if W>W.threshold or equivalently, q-value<fdr threshold. There is no significant gene if W.threshold=Inf.
Qvalue	The q-values for each gene.
gene_sign	Significant genes with q-values less then the fdr threshold.

Examples

library(GeneScan3DKnock)

# Load data example
data("GeneScan3DKnock.example")

result.GeneScan3DKnock=GeneScan3DKnock(M=5,
p0=GeneScan3DKnock.example$GeneScan3D.original,
p_ko=cbind(GeneScan3DKnock.example$GeneScan3D.ko1,
          GeneScan3DKnock.example$GeneScan3D.ko2,
          GeneScan3DKnock.example$GeneScan3D.ko3,
          GeneScan3DKnock.example$GeneScan3D.ko4,
          GeneScan3DKnock.example$GeneScan3D.ko5),fdr = 0.1,
          gene_id=GeneScan3DKnock.example$gene.id)
result.GeneScan3DKnock$W
result.GeneScan3DKnock$W.threshold
result.GeneScan3DKnock$Qvalue
result.GeneScan3DKnock$gene_sign

Iuliana-Ionita-Laza/GeneScan3DKnock documentation built on July 31, 2023, 4:32 a.m.