ct.RRAaPvals: gRNA signal aggregation via RRAa

Description Usage Arguments Value Author(s) Examples

View source: R/RRAalpha.R

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

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ct.RRAaPvals(p, g.key, permute, permutation.seed = 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.

Value

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

Author(s)

Russell Bainer

Examples

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

gCrisprTools documentation built on May 31, 2017, 11:42 a.m.

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