geneClass: Retrieve the regulatory class for each gene

In INSPEcT: Modeling RNA synthesis, processing and degradation with RNA-seq data

Description

This method returns a factor that summarise the gene class (transcriptional regulatory mechanism) that INSPEcT has assigned to each gene. The variability of each rate is indicated with a letter, 's' for synthesis, 'p' for processing and 'd' for degradation. In case more than one rate is variable, the letters associated to each variable rate are merged, for example 'sd' stands for a gene where synthesis and degradation cotributed to transcriptional changes. 'no-reg' is associated to genes with no change in transcription. The classification depends on the thresholds of the goodness-of-fit and rate variability tests that can be changed via the method calculateRatePvals.

Usage

geneClass(object, ...)

## S4 method for signature 'INSPEcT'
geneClass(object, ...)

## S4 method for signature 'INSPEcT_model'
geneClass(object, ...)

## S4 method for signature 'INSPEcT_diffsteady'
geneClass(object, ...)

Arguments

object	An object of class INSPEcT or INSPEcT_model
...	specify the threshold for rate variability 'bTsh' in case of 'INSPEcT_diffsteady' objects (default = .1)

Value

A character containing the regulatory class for each gene

See Also

ratePvals

Examples

nascentInspObj10 <- readRDS(system.file(package='INSPEcT', 'nascentInspObj10.rds'))
geneClass(nascentInspObj10)
# see the classification with another threshold for rate variability
nascentInspObj10 <- calculateRatePvals(nascentInspObj10, p_variability=rep(1,3))
geneClass(nascentInspObj10)

INSPEcT documentation built on Nov. 8, 2020, 6:49 p.m.