calculateGenePval {CEDA}

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.