seq_alignment: Functions Related to Sequence Alignment

In krm: Kernel Based Regression Models

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.

krm documentation built on Oct. 18, 2022, 9:09 a.m.