calculateGenePval: Calculating gene level p-values using modified robust rank...

In CEDA: CRISPR Screen and Gene Expression Differential Analysis

Calculating gene level p-values using modified robust rank aggregation (alpha-RRA method) on sgRNAs' p-values

Description

Code was adapted from R package gscreend. The alpha-RRA method is adapted from MAGeCK.

Usage

calculateGenePval(pvec, genes, alpha, nperm = 20)

Arguments

pvec	A numeric vector containing p-values of sgRNAs.
genes	A character string containing gene names corresponding to sgRNAs.
alpha	A numeric number denoting the alpha cutoff (i.e. 0.05).
nperm	Number of permutations, default is 20

Value

A list with four elements: 1) a list of genes with their p-values; 2) a numeric matrix of rho null, each column corresponding to a different number of sgRNAs per gene; 3)a numeric vector of rho; 4) a numeric vector of number of sgRNAs per gene.

CEDA documentation built on May 29, 2024, 7:44 a.m.