calConservation

calConservation-methods

calConservation,character,character-method

calConservation,character,missing-method

calConservation,DNAString,DNAString-method

calConservation,DNAStringSet,missing-method


    A <code>DNAString</code> object , a <code>DNAStringSet</code> or a <code>character</code> object, 
    which contains the pairwise alignments.
    When the last two objects have a length of 2, the argument <code>aln2</code> can be missing.
  

aln1


    A <code>DNAString</code>, a <code>character</code> object or missing.
  

aln2


    The size of the sliding window (in nucleotides) for calculating local conservation in the alignment. This should be an odd value.
  

windowSize


    The conservation profile of Which sequence in the alignments is computed. It can be "1" or "2".
  

which


  Calculate the conservation score for a pairwise alignment given a smooth window size.


methods

TFBSTools is a package for the analysis and manipulation of
transcription factor binding sites. It includes matrices conversion
between Position Frequency Matirx (PFM),
Position Weight Matirx (PWM) and Information Content Matrix (ICM).
It can also scan putative TFBS from sequence/alignment,
query JASPAR database and provides a wrapper of
de novo motif discovery software.

Ge Tan

TFBSTools

Software Package for Transcription Factor Binding Site (TFBS) Analysis

calConservation-methods function

A <code>DNAString</code> object , a <code>DNAStringSet</code> or a <code>character</code> object, 
    which contains the pairwise alignments.
    When the last two objects have a length of 2, the argument <code>aln2</code> can be missing.

A <code>DNAString</code>, a <code>character</code> object or missing.

The size of the sliding window (in nucleotides) for calculating local conservation in the alignment. This should be an odd value.

The conservation profile of Which sequence in the alignments is computed. It can be "1" or "2".

Calculate the conservation score for a pairwise alignment given a smooth window size.

calConservation-methods: calConservation method

Description

Usage

Arguments

Value

See Also