filterOverlap: function to filter probe sequence overlaps and remap probes

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

Description

This function remaps the probe sequence to a reference sequence and filters probe sequence overlaps between PM and MM probes and/or between probes on the forward and reverse strand

Usage

filterOverlap(object, remap = TRUE, BSgenomeObject, chrId, strand = c("forward","reverse","both"), MM=FALSE, ...)

Arguments

object	object of class WaveTilingFeatureSet
remap	logical to determine whether the tiling array probe sequences have to be remapped to a more recent reference DNA sequence
BSgenomeObject	object of class BSgenome containing the genome sequence of the species for which the probes need to be filtered and remapped
chrId	vector of numerics identifying the chromosomes for which the probes have to be filtered and/or remapped
strand	character indicating the strands for which the probes have to be filtered and/or remapped (forward, reverse or both)
MM	logical to indicate whether the tiling array contains MM probes or not
...	other arguments

Value

An object of class mapFilterProbe is returned containing the indices of the filtered probes.

Author(s)

Kristof De Beuf <[e-mail]>

Examples

## Not run: 
  data(leafdev)
  as(leafdev,"WaveTilingFeatureSet")
  library(BSgenome.Athaliana.TAIR.TAIR9)
  leafdevMapAndFilterTAIR9 <- filterOverlap(leafdev,remap=TRUE,BSgenomeObject=Athaliana,chrId=1:7,strand="both",MM=FALSE)

## End(Not run)

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