gemini_score: Scoring Combination Effect

Description Usage Arguments Value Examples

View source: R/gemini_score.R

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

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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

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

sellerslab/gemini documentation built on April 9, 2021, 9:01 p.m.