calConservation-methods: calConservation method
In ge11232002/TFBSTools: Software Package for Transcription Factor Binding Site (TFBS) Analysis

calConservation-methods

R Documentation

calConservation method

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

  calConservation(aln1, aln2, windowSize=51L, which="1")

`aln1`	A `DNAString` object , a `DNAStringSet` or a `character` object, which contains the pairwise alignments. When the last two objects have a length of 2, the argument `aln2` can be missing.
`aln2`	A `DNAString`, a `character` object or missing.
`windowSize`	The size of the sliding window (in nucleotides) for calculating local conservation in the alignment. This should be an odd value.
`which`	The conservation profile of Which sequence in the alignments is computed. It can be "1" or "2".

A numeric vector with the same length of alignment is returned.

Ge Tan