DIPA: Dynamic promoter activity.

In soumyakannan/promact: Dynamic Inference of Promoter Activity

Description

DIPA returns a vector of promoter activity over specified times as described in PUBLICATION NAME.

Usage

DIPA(x, t.f, f.data, t.b, b.data, m = log(2)/0.45, d = log(2)/0.5,
  beta = 1, d.r = 1, data.type = 3)

Arguments

x	Vector of times over which to calculate promoter activity (in hours).
t.f	Vector of times of reporter protein (or mRNA) measurements (in hours).
f.data	Vector of of reporter protein (or mRNA) measurements.
t.b	Vector of times of biomass measurements (in hours).
b.data	Vector of biomass measurements.
m	Maturation constant (if using fluorescent protein reporter). Defaults to log(2)/0.45 h^-1.
d	Degradation rate of protein. Defaults to log(2)/0.5 h^-1 (Mateus & Avery 2000).
beta	Translation rate. Defaults to 1.
d.r	mRNA degradation rate. Defaults to 1.
data.type	Indicates type of input data, with numbers corresponding to number of ODEs necessary to model the reporter system. 1 = mRNA, 2 = protein other than fluorescent (i.e. luciferase, beta-galactosidase, etc.), 3 = fluorescent protein (i.e. GFP, RFP, etc). For more information, see references. Defaults to 3.

Details

This function requires reporter protein data and corresponding time points, and biomass data and corresponding time points stored in R vectors or similar data structure. User can choose the nature of input (fluorescent protein, other protein or mRNA) data via the data.type input. For single-cell data, input biomass as a vector of 1's of corresponding length to gene expression measurements, and consider promoter activity output to be activity per cell.

Value

Returns a list L with L$t the time series input by the user and L$promact the calculated promoter activities at these times.

Author

Soumya Kannan, Technical University of Denmark, 2017.

References

PUBLICATION CITATION.

soumyakannan/promact documentation built on May 8, 2019, 9:24 a.m.