Get_params: Getting the parameters for simulating gene expression from...

In YosefLab/SymSim: Simulate Single Cell RNA Sequencing Data

Getting the parameters for simulating gene expression from EVf and gene effects

Description

This function takes gene_effect and EVF, take their dot product and scale the product to the correct range by using first a logistic function and then adding/dividing by constant to their correct range

Usage

Get_params(gene_effects, evf, match_param_den, bimod, scale_s)

Arguments

gene_effects	a list of three matrices (generated using the GeneEffects function), each corresponding to one kinetic parameter. Each matrix has nevf columns, and ngenes rows.
evf	a vector of length nevf, the cell specific extrinsic variation factor
match_param_den	the fitted parameter distribution density to sample from
bimod	the bimodality constant
scale_s	a factor to scale the s parameter, which is used to tune the size of the actual cell (small cells have less number of transcripts in total)

Value

params a matrix of ngenes * 3

Examples

Get_params()

YosefLab/SymSim documentation built on Sept. 30, 2024, 2:22 p.m.