Description Usage Arguments Value Examples

View source: R/newINSPEcT-functions.R

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.

1 2 3 4 |

`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 |

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

`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 2/3 of the observations |

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

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | ```
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)
``` |

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