GenehitsCaller: GenehitsCaller

In chenweng1991/CrisprScreen:

Description

This function allows you to collapse sgRNA into gene in order to identify gene hits.

Usage

GenehitsCaller(enrichment.data = P5.P6.enrichment, Tier1Cut = 0.001,
  Tier2Cut = 0.01, Tier1Nmin = 1, TotalNmin = 2,
  conflict = "Onlytier1")

Arguments

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 will return a list of two dataframe including gene hits that show the number of supporting sgRNA; and tier1+tier2 sgRNA data of all hits genes

Examples

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

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