INSPEcT_steadyNoNascent-class: An S4 class to represent steady-state analysis without...

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

Description

INSPEcT_steadyNoNascent is a class able to store data and arguments that are necessary to make the analysis concerning premature and mature expressions in different samples. In particular, the ratio between mature and premature can be calculated, which reflects the ratio between the rates of processing and degradation in individaul genes (see PTratio), and the analysis of post-transcriptionally regualted genes can be run to identify genes that in specfic samples show a trand which cannot be attributed to transcriptional regulation alone (see PTreg).

Usage

## S4 method for signature 'INSPEcT_steadyNoNascent,ANY,ANY,ANY'
x[i, j]

## S4 method for signature 'INSPEcT_steadyNoNascent'
show(object)

Arguments

x	An object of class INSPEcT_steadyNoNascent
i	A numeric, a vector of logicals indicating the rows to be extracted
j	A numeric, a vector of logicals indicating the columns to be extracted
object	An object of class INSPEcT_steadyNoNascent

Value

Method show for objects of class INSPEcT_steadyNoNascent

Slots

sampleNames

Vector with the names of the samples (columns of the dataset)

geneNames

Vector with the names of the genes (rows of the dataset)

premature

Matrix containing the expressions of the premature RNAs (row=genes, columns=samples)

mature

Matrix containing the expressions of the emature RNAs (row=genes, columns=samples)

prematureVar

Matrix containing the expressions variances of the premature RNAs (row=genes, columns=samples)

matureVar

Matrix containing the expressions variances of the emature RNAs (row=genes, columns=samples)

trivialAngle

Numeric that indicates the angle (slope) of the linear model between mature and premature expressions

log2FCThreshold

Numeric that describes the threshold of the variation to be considered significant

expressionThreshold

Numeric that describes the threshold of the expression to consider the gene expressed

referenceCondition

A sample identifier that set the reference for the post-transcriptional regulation analysis, if NULL the median of all samples is used

ptreg

Matrix containing the post-transcriptioanl regulation state of each gene in the different samples (row=genes, columns=samples)

ste-depo/INSPEcT documentation built on Oct. 3, 2020, 9:14 p.m.