ct.RRAaPvals: gRNA signal aggregation via RRAa

In gCrisprTools: Suite of Functions for Pooled Crispr Screen QC and Analysis

Description

This is a wrapper function implementing the RRAalpha p-value aggregation algorithm. Takes in a set of gRNA rank scores (formatted as a single-column numeric matrix with row.names indicating the guide names) and a list object of gRNA annotations (names are the gene targets, and each element of the list contains a vector of the corresponding guide names). The rank scores are converted to gene-level statistics that are thenm transformed into empirical p-values by permutation.

Usage

ct.RRAaPvals(p, g.key, permute, permutation.seed = NULL, multi.core = NULL)

Arguments

p	A single column matrix of ranking scores, with row.names indicating the gRNA labels
g.key	An annotation data frame of gRNAs, minimally containing a factorized "geneSymbol" column indicating the target names. This is typically generated by calling the ct.buildKeyFromAnnotation() function.
permute	Number of permutations to be used during empirical p-value estimation.
permutation.seed	numeric seed for permutation reproducibility. Default: NULL means to not set any seed.
multi.core	Deprecated, does nothing

Value

A named list of target-level empirical P-values.

Author(s)

Russell Bainer

Examples

data('fit')
data('ann')
genePvals <- ct.RRAaPvals(fit$p.value, ann, permute = 100)

gCrisprTools documentation built on Nov. 8, 2020, 8:17 p.m.