gemini_score {gemini} | R Documentation

## Scoring Combination Effect

### Description

Score genetic interactions from a gemini.model and produce a gemini.score object, and generate p-values and FDRs if negative control pairs (`nc_pairs`) are available.

### Usage

    gemini_score(
      Model,
      pc_gene = NA,
      pc_threshold = NULL,
      pc_weight = 0.5,
      nc_pairs = NA
    )

### Arguments

`Model` | an object of class gemini.model
`pc_gene` | a character vector of any length naming genes to use as positive controls
`pc_threshold` | a numeric value to indicate the LFC corresponding to a positive control, if no pc_gene is specified.
`pc_weight` | a weighting applied to the positive control (`pc_gene`) to filter genes whose individual phenotype is more lethal than pc_weight*y(pc_gene).
`nc_pairs` | a set of non-interacting gene pairs to define statistical significance.

### Value

An object of class gemini.score containing score values for strong interactions and sensitive lethality and recovery, and if `nc_pairs` is specified, statistical significance for each scoring type.

### Examples

    data("Model", package = "gemini")
    Score <- gemini_score(Model, pc_gene = "EEF2")

[Package gemini version 1.8.0 Index]