Inject an external cell context into the model as the control baseline of the following

set_context {GPS}

R Documentation

Inject an external cell context into the model as the control baseline of the following

Description

in silico perturbation experiments.

Usage

set_context(gps, genes, logcpm);

Arguments

gps

the trained model object. [as GPSModel]

genes

a character vector of the gene id of the context profile; the ids must live in the same identifier space as the model (Ensembl gene id for the human model).

logcpm

a numeric vector of the log2(CPM + 1) expression value of the context, in the same order as genes. The caller is responsible for the library size normalization and for the log transform; the model only applies its own z-score.

env

the R# runtime environment. [as Environment]

Details

Genes of the model that are missing from genes keep their own mean (that is a z-score of zero), so a context is allowed to cover only the genes of the sequencing panel.

Authors

biosystem

Value

TRUE when the context has been applied; an R# error message object is returned when the gene ids do not overlap the modelled genes at all.

clr value class

any kind

[Package GPS version 1.0.0.0 Index]