Description Usage Arguments Value Examples
View source: R/ComputeGlobalFDR.R
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
1 2 3 | ComputeGlobalFDR(enrichment.data = P5.P6.enrichment, Tier1Cut = 0.001,
Tier2Cut = 0.01, Tier1Nmin = 1, TotalNmin = 2,
conflict = "Alltiers", shuffN = 100)
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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 |
This function will return a vector that include three component: expected gene hits number by permutation; observed gene hits nuber; global FDR
1 | sgRNAdistribute(enrichment.data=P5.P6.enrichment)
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