pulseTDmodel-class: pulseTD-model

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

Description

'pulseTD-model' is S4 class for storing calculation results. It includes pulse model parameters corresponding to transcription rate, processing rate and degradation rate, and also stores some basic parameters of the calculation process, such as gene name, sequencing time, labeling time and so on.

Slots

genenames

All gene names entered by the user.

t_time

Storage time series.

tL

4sU labeled duration

fitfailure

Gene vector for parameter optimization failure

filterExpression.foursu_exons

'AnnotatedDataFrame' that stores 4sU-labeled exons expression values

filterExpression.total_exons

'AnnotatedDataFrame' that stores total exons expression values

filterExpression.total_introns

'AnnotatedDataFrame' that stores total introns expression values

ratesPar.degradation

'AnnotatedDataFrame' that stores degradation pulse parameters

ratesPar.processing

'AnnotatedDataFrame' that stores processing pulse parameters

ratesPar.transcription

'AnnotatedDataFrame' that stores transcription pulse parameters

ratesPar.score

'AnnotatedDataFrame' that stores the fit scores

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