pulseModel: pulse function

In pulseTD: Identification of Transcriptional Dynamics using Pulse Models via 4su-Seq Data and RNA-Seq Data

Description

Pulse function is a pulse function J Comput Biol (2009 Feb) <doi:10.1089/cmb.2008.13TT>. This is a multiplication of two sigmoid functions, the parameter vector Theta = (h0, h1, h2, t1 t2, beta), where h0, h1, h2, represent the initial state rate value, peak value and the steady state rate value is reached again, t1 and t2 are the maximum times of the first and second rise or fall changes, respectively, and beta is the slope of the two changes.

Usage

pulseModel(xita, x)

Arguments

xita	Six parameters of the pulse function :h0, h1, h2, t1, t2, beta. Details getParams
x	a vector or point of time

Value

a vector or point of pulse function value

Examples

load(file.path(system.file(package="pulseTD"),"data","pulseRates.RData"))
TimeGrid <- c(0, 15, 30, 45, 60, 75, 90, 105, 120, 135, 150, 165, 180)
pulseRates_correct <- correctionParams(pulseRates)
transcription_params = getParams(pulseRates_correct,'transcription')
degradation_params = getParams(pulseRates_correct, 'degradation')
processing_params = getParams(pulseRates_correct, 'processing')
###
transcription_pulse = pulseModel(as.matrix(transcription_params[1,]), TimeGrid)
degradation_pulse = pulseModel(as.matrix(degradation_params[1,]), TimeGrid)
processing_pulse = pulseModel(as.matrix(processing_params[1,]), TimeGrid)

pulseTD documentation built on May 17, 2019, 5:03 p.m.