Create a new INSPEcT object

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Description

The function newINSPEcT creates a new instance of the class INSPEcT, provided the intronic and exonic RPKMs of RNA- and 4sU-seq experiments at different time points, the time points, the labeling time and optionally the scaling factor to normalize the libraries. The scaling factor to normalize the 4sU-seq libraries can be calculated by the function itself and this way of calulating the scaling factors gives robustness to the estimation of sythesis, degradation and processing rates. In case only exonic RPKMs are provided, only synthesis and degradation rates can be estimated by the function newINSPEcT and the scaling factors to normalize 4sU-seq libraries cannot be caluculated. To provide robustness to the procedure the argument labeledSF is strongly suggested in this case.

Usage

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newINSPEcT(tpts, labeling_time, rpkms_4su_exons, rpkms_total_exons,
  rpkms_4su_introns = NULL, rpkms_total_introns = NULL,
  BPPARAM = bpparam(), totalMedianNorm = TRUE, labeledMedianNorm = FALSE,
  totalSF = NULL, labeledSF = NULL, totalQuantileNorm = FALSE,
  labeledQuantileNorm = FALSE, simulatedData = FALSE,
  degDuringPulse = FALSE)

Arguments

tpts

A vector of time points

labeling_time

A number, lenght of the 4sU pulse

rpkms_4su_exons

A matrix containing expression levels of 4su exons

rpkms_total_exons

A matrix containing expression levels of total exons

rpkms_4su_introns

A matrix containing expression levels of 4su introns

rpkms_total_introns

A matrix containing expression levels of total introns

BPPARAM

Configuration for BiocParallel parallelization. By default is set to bpparam()

totalMedianNorm

A logical to perform median normalization over total RNA exons rpkms, it will apply also on introns

labeledMedianNorm

A logical to perform median normalization over 4sU RNA exons rpkms, it will apply also on introns

totalSF

A vector storing user defined normalization scale over Total RNA exons and introns rpkms

labeledSF

A vector storing user defined normalization scale over 4sU RNA exons and introns rpkms

totalQuantileNorm

A logical to perform to perform median normalization over total RNA exons rpkms, it will apply also on introns

labeledQuantileNorm

A logical to perform to perform median normalization over 4sU RNA exons rpkms, it will apply also on introns

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

Value

An object of class INSPEcT with rates guessed, rates can be accessed by ratesFirstGuess method.

Examples

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data('rpkms', package='INSPEcT')
tpts <- c(0, 1/6, 1/3, 1/2, 1, 2, 4, 8, 16)
tL <- 1/6
mycerIds <- newINSPEcT(tpts, tL, rpkms$foursu_exons, rpkms$total_exons, 
	rpkms$foursu_introns, rpkms$total_introns, BPPARAM=SerialParam())

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