newINSPEcT {INSPEcT} | R Documentation |
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.
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 )
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. |
An object of class INSPEcT with a first estimation of the rates which can be accessed by the method ratesFirstGuess
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)