getRates: Get rate values

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

Description

It is used to calculate the transcriptional dynamic rate of a gene. You can get the discrete or continuous rate values of the measurement time points. At the same time, it has a predictive function that provides rate values for any future time node or any range of time.

Usage

getRates(object, stage, timevector = NULL, genename = NULL)

Arguments

object	a 'pulseTDmodel' that has been calculated with estimateParams
stage	A character is one of three stages of transcriptional dynamics, transcription, processing and degradation.
timevector	A vector of time, which can be any time, defaults to NULL If it is NULL: only calculate the transcriptional dynamics of the measurement time node, the time is obtained by t_time in pulseTDmodel If the time vector is positive: calculate the rate value for a given time, or the predicted rate if the time exceeds the measurement time node If the time vector is negative: Calculate the rate value at a given time, which represents the calculation of the transcriptional dynamic rate before the prediction of the experimental measurement.
genename	a vector, default is NULL If it is NULL: Calculate the transcriptional dynamic rate of all genes If it is a gene vector: only calculate the transcriptional dynamic rate of a given gene vector If it is a numerical vector: only calculate the transcriptional dynamic rate of the gene corresponding to a given value.

Value

A matrix, each row representing a gene, each column with a table to calculate the time node, and the value representing the rate of transcriptional dynamics.

Examples

load(file.path(system.file(package="pulseTD"),"data","pulseRates.RData"))
pulseRates_correct <- correctionParams(pulseRates)
transcription = getRates(pulseRates_correct,'transcription')
degradation = getRates(pulseRates_correct, 'degradation')
processing = getRates(pulseRates_correct, 'processing')
head(transcription)
head(degradation)
head(processing)
trans = getRates(pulseRates_correct, 'transcription', timevector=c(0,1,2,3))
head(transcription)
trans=getRates(pulseRates_correct, 'transcription', timevector=c(2,3),genename=c(2,3))
head(transcription)

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