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

In RGBM: LS-TreeBoost and LAD-TreeBoost for Gene Regulatory Network Reconstruction

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 <[e-mail]>

See Also

null_model_refinement_step, z_score_effect

RGBM documentation built on April 14, 2023, 9:10 a.m.