| get_ko_experiments {RGBM} | R 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