ComputeGlobalFDR: ComputeGlobalFDR

In chenweng1991/CrisprScreen:

Description

This function allows you compute the global FDR by permutation to evaluate the reliability of the gene hits. The parameter is exactly the same as GenehitsCaller

Usage

ComputeGlobalFDR(enrichment.data = P5.P6.enrichment, Tier1Cut = 0.001,
  Tier2Cut = 0.01, Tier1Nmin = 1, TotalNmin = 2,
  conflict = "Alltiers", shuffN = 100)

Arguments

enrichment.data	The data prepared by "ComputeEnrichment"
Tier1Cut	The pvalue/FDR cutoff below which an sgRNA is considered tier1 sgRNA(very significant)
Tier2Cut	The pvalue/FDR cutoff between which to Tier1Cut an sgRNA is considered tier2 sgRNA(Somewhat significant)
Tier1Nmin	Minimum number of supporting Tier1 sgRNA required to identify a gene hit (1,2,3,4,5,6)
TotalNmin	Minimum number of supporting Tier1+Tier2 sgRNA required to identify a gene hit (1,2,3,4,5,6)
conflict	When getting rid of genes with conficting significant sgRNA. i,e. sgRNA show opposite direction. if "Onlytier1" then only consider confliction in Tier1 if "Alltiers" then consider both tier1 and tier2

Value

This function will return a vector that include three component: expected gene hits number by permutation; observed gene hits nuber; global FDR

Examples

sgRNAdistribute(enrichment.data=P5.P6.enrichment)

chenweng1991/CrisprScreen documentation built on July 12, 2019, 11:42 a.m.