get_ko_experiments: Get indices of experiments where knockout or knockdown...

View source: R/proposed_steps.R

get_ko_experimentsR Documentation

Get indices of experiments where knockout or knockdown happened

Description

This function provides the indices of all those samples (out of N) where it is known apriori that a gene was either knocked-out or was knocked-down. This information is useful for the null_model_refinement_step which utilizes the z_score_effect technique (with the help of this information).

Usage

get_ko_experiments(K)

Arguments

K

N-by-p initial perturbation matrix. It directly corresponds to E matrix, e.g. if K[i,j] is equal to 1, it means that gene j was knocked-out in experiment i. Single gene knock-out experiments are rows of K with only one value 1. Colnames of K is set to be the set of all genes. By default it's a matrix of zeros of the same size as E, e.g. unknown initial perturbation state of genes.

Value

Return a vector containing the indices of all the samples where a gene was knocked-out/down.

Author(s)

Raghvendra Mall <rmall@hbku.edu.qa>

See Also

null_model_refinement_step, z_score_effect


RGBM documentation built on Aug. 11, 2022, 5:10 p.m.