ct.RRAaPvals {gCrisprTools} | R Documentation

## gRNA signal aggregation via RRAa

### 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)

[Package gCrisprTools version 1.12.0 Index]