calcPairwiseIdentity {krm}

Functions Related to Sequence Alignment

Description

Functions related to sequence alignment

Usage

calcPairwiseIdentity(alignment, dissimilarity, removeGap)
alignment2count (alignment, level=20, weight=rep(1,nrow(alignment)))
alignment2trancount (alignment, weight=rep(1,nrow(alignment)))
removeGap (seq) 

Arguments

alignment

matrix of arabic representation of sequences (1 based)

dissimilarity

Boolean.

removeGap

Boolean

level

integer. Size of alphabet

weight

numeric vector. Weights given to each sequence

seq

string. A string of amino acids

Value

alignment2count return T by 20 matrix, where T is the number of column in the alignment. alignment2trancount return a T by 4 matrix, each row is the count of MM, MD, DM, DD for each position.