newINSPEcT: Create a new INSPEcT object

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

Description

The function newINSPEcT creates a new instance of the class INSPEcT provided the experimental time points, expression data (like RPKMs) of mature and eventually nascent RNA. For the nascent analysis, it is also requires a collecting time and the scaling factor to normalize the nascent RNA-seq libraries. This latter parameter can also be calculated by the function itself if both exonic and intronic expression data are provided; otherwise it must be given as an input and it is essential to guarantee the robustness of the analysis.

Usage

newINSPEcT(
  tpts,
  labeling_time = NULL,
  nascentExpressions = NULL,
  matureExpressions,
  preexisting = FALSE,
  BPPARAM = SerialParam(),
  labeledSF = NULL,
  simulatedData = FALSE,
  degDuringPulse = FALSE,
  Dmin = 1e-06,
  Dmax = 10,
  genesFilter = TRUE,
  genesFilterThreshold = 2/3,
  imputeNAs = TRUE
)

Arguments

tpts	A vector of time points, one for each sample
labeling_time	A number, lenght of the Nascent pulse
nascentExpressions	A list which contains exons and introns expression matrices and variances for the nascent RNA
matureExpressions	A list which contains exons and introns expression matrices and variances for the mature RNA
preexisting	A logical, indicating if the mature expression refers to the pre-exising (unlabeled) population. Not implemented yet for the "degDuringPulse" mode.
BPPARAM	Configuration for BiocParallel parallelization. By default is set to SerialParam()
labeledSF	A vector storing user defined normalization scale over Nascent RNA exons and introns quantifications
simulatedData	A logical, set to TRUE in case the analysis is on simulated data
degDuringPulse	A logical, set to TRUE in case of a long labelling time. Also degradation of newly synthesized transcripts will be taken into account
Dmin	A numerical, it is the lower bound of the degradation rate domain for the prior optimization
Dmax	A numerical, it is the upper bound of the degradation rate domain for the prior optimization
genesFilter	A logical, if TRUE, filters out genes which have no signal in at least a given fraction (2/3 by default) of the observations
genesFilterThreshold	A number, threshold to use for genes filtering (2/3 by default)
imputeNAs	A logical, if TRUE the rates first guess which are not finite are imputed from the neighbours.

Value

An object of class INSPEcT with a first estimation of the rates which can be accessed by the method ratesFirstGuess

Examples

data('allcounts', package='INSPEcT')
data('featureWidths', package='INSPEcT')
data('libsizes', package='INSPEcT')

matureCounts<-allcounts$mature
tpts <- c(0,1/6,1/3,1/2,1,1.5,2,4,8,12,16)
expDes<-rep(tpts,3)

matExp_DESeq2<-quantifyExpressionsFromTrCounts(
 	allcounts=matureCounts
 	,libsize=totalLS
 	,exonsWidths=exWdths
 	,intronsWidths=intWdths
 	,experimentalDesign=expDes)

matureInspObj<-newINSPEcT(tpts=tpts
                         ,labeling_time=NULL
                         ,nascentExpressions=NULL
                         ,matureExpressions=matExp_DESeq2)

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