createVariants: Create variants for genes in the system.

In oliviaAB/sismonr: Simulation of in Silico Multi-Omic Networks

Create variants for genes in the system.

Description

Create variants that segregate in the in silico population for each gene in the system.

Usage

createVariants(genes, indargs)

Arguments

genes	A data frame of genes in the system (created by the function createGenes).
indargs	An object of class insilicoindividualargs (i.e. a list with parameters for in silico individuals generation).

Value

A list of size G (number of genes in the system) where each element is a matrix corresponding to the QTL effect coefficients (rows) of the different variants (columns) segregating in the in silico population for the corresponding gene. A variant is defined by a set of QTL effect coefficients ("qtlTCrate", "qtlRDrate", "qtlTCregbind", "qtlRDregrate", "qtlactivity", "qtlTLrate", "qtlPDrate", "qtlTLregbind", "qtlPDregrate") that correspond to the impact of genetic mutations carried by the variant on the different kinetic parameters of the gene, as follow:

• qtlTCrate: affects the basal transcription rate of the gene;

• qtlRDrate: Affects the basal RNA decay rate of the gene;

• qtlTCregbind: Affects the binding rate of the regulators of transcription on the gene's promoter (affects all transcription regulators targeting this gene);

• qtlRDregrate: Affects the rate at which regulators of RNA decay encountering the RNAs of the gene trigger their degradation (affects all RNA decay regulators targeting this gene);

• qtlactivity: Affects the activity of the active product of the gene. If the gene is encoding for a regulator of transcription or translation, this affects the binding rate of its active products (i.e. RNAs or proteins) to their binding sites on their targets (affects the binding to all targets of the gene). If the gene encodes a regulator of RNA or protein decay or of protein post-translational modification, this affects the rate at which its active products (i.e. RNAs or proteins) trigger the degradation/transformation of their targets (effect for all targets of the gene);

• qtlTLrate: Affects the basal translation rate of the gene;

• qtlPDrate: Affects the basal protein decay rate of the gene;

• qtlTLregbind: Affects the binding rate of the regulators of translation on the gene's RNA binding sites (affects all translation regulators targeting this gene);

• qtlPDregrate: Affects the rate at which regulators of protein decay encountering the proteins of the gene trigger their degradation (affects all protein decay regulators targeting this gene);

• qtlPTMregrate: Affects the rate at which regulators of protein post-translational modification encountering the proteins of the gene trigger their modification (affects all protein post-translational modification regulators targeting this gene).

Examples

indargs = insilicoindividualargs()
genes = createGenes(insilicosystemargs(G = 5))
variants = createVariants(genes, indargs)

oliviaAB/sismonr documentation built on June 25, 2022, 11:59 p.m.