Run the perturbation experiment for a set of genes and collect the profiles into a matrix.

profiles_matrix {linear}

R Documentation

Run the perturbation experiment for a set of genes and collect the profiles into a matrix.

Description

Usage

profiles_matrix(model, genes,
    mode = "knockdown");

Arguments

model

the perturbation engine that is created via elastic_model. [as ElasticNet]

genes

the target gene ids, one column will be generated for each of them

mode

knockout, knockdown (default) or overexpress. [as string]

env

the R# runtime environment object. [as Environment]

Details

This api is the memory friendly replacement of the make_exports api for a batch run: it does not generate the ten difference analysis tables for every condition.

Authors

TRNtoolkit

Value

a matrix of the [gene x condition] mutant means. The genes that can not be found in the model are skipped, so the column number equals the number of the matched genes.

clr value class

Matrix

[Package linear version 1.0.0.0 Index]