calConservation-methods: calConservation method

In TFBSTools: Software Package for Transcription Factor Binding Site (TFBS) Analysis

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

TFBSTools documentation built on Nov. 8, 2020, 8:14 p.m.