getSigGenes {waveTiling} | R Documentation |
Extract the annotated regions (often genes) that overlap with the significant regions found in the wavelet-based transcriptome analysis.
getSigGenes(fit,inf,biomartObj)
fit |
object of class |
inf |
object of class |
biomartObj |
object of class TxDb representing an annotation database generated from BioMart. |
GRangesList object. In the elementMetadata of the GRanges elements percOverGene
gives the percentage of basepair overlap of the annotated regions by the detected significant region in the analysis; percOverReg
gives the percentage of basepair overlap of the detected singificant region in the analysis with the annotated region; totPercOverGene
gives per annotated region the total percentage of basepair overlap by all detected significant regions in the analysis that map to that annotated region.
Kristof De Beuf <kristof.debeuf@ugent.be>
library(waveTilingData) library(TxDb.Athaliana.BioMart.plantsmart22) data(leafdevFit) data(leafdevInfCompare) sigGenesCompare <- getSigGenes(fit=leafdevFit,inf=leafdevInfCompare, biomartObj=TxDb.Athaliana.BioMart.plantsmart22) head(sigGenesCompare[[2]])