calConservation-methods {TFBSTools} | R Documentation

## calConservation method

### Description

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

### Usage

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

### Arguments

`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".

### Value

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

### Author(s)

Ge Tan

### See Also

`searchAln`

[Package TFBSTools version 1.18.0 Index]