pulseTD (version 0.1.0)

getRates: Get rate values

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

# NOT RUN {
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)
# }