getSigGenes: Get significant genes

In waveTiling: Wavelet-Based Models for Tiling Array Transcriptome Analysis

Description

Extract the annotated regions (often genes) that overlap with the significant regions found in the wavelet-based transcriptome analysis.

Usage

getSigGenes(fit,inf,biomartObj)

Arguments

fit	object of class WfmFit
inf	object of class WfmInf
biomartObj	object of class TxDb representing an annotation database generated from BioMart.

Value

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.

Author(s)

Kristof De Beuf <[e-mail]>

Examples

  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]])

waveTiling documentation built on Oct. 31, 2019, 9:23 a.m.