ceScanOneStep


  The <code>axt</code> object or axt filenames with each assembly as referecne.
 

axt1,axt2


  The <code>GRanges</code> object or bed filenames.
 

filter1,filter2


  A <code>Seqinfo</code> object which contains the <code>seqnames</code> and
    <code>seqlengths</code> for each assembly.
 

sizes1,sizes2

assembly1,assembly2


  The file names of two bit files of two assemblies.
 

twoBit1,twoBit2


    A <code>character</code> object specifiying the scanning windows and
    minimal score.
    It can be specified in th form of "45_50" with scanning windows 50
    and minial score 45.
    More than one thresholds can be provided.
 

thresholds


 A object of <code>character</code>. The path of blat binary.
 

blatBinary


  A object of <code>integer</code>.
  The CNEs with more than the cutoff hits on the reference genome are removed.
 

blatCutoff1, blatCutoff2


This function run cne detection in one function.


Large-scale identification and advanced visualization
of sets of conserved noncoding elements.

ceScanOneStep: ceScanOneStep function

Description

Usage

Arguments

Value