Submatrix-class: Class "Submatrix" Substitution Matrix

In wolski/pairseqsim: pairwise sequence alignment similarity simple.

Description

Amino Acid Substitution Matrices

Objects from the Class

new("Submatrix", ...). or data(EPAM100

Slots

.Data:

Object of class "matrix" substitution matrix

copyright:

Object of class "character" GNU GPL2

info:

Object of class "character" name

head:

Object of class "character" description

alphabet:

Object of class "character" alphabet

Extends

Class "matrix", directly.

Methods

selfalign

signature(object = "AASequence", sub = "Submatrix"): compute teh score for aligning the sequence with itself

show

signature(object = "Submatrix"): show

subFromEmboss

signature(object = "Submatrix", path = "character"): read Substitution matrices from EMBOSS package

Author(s)

Witold Eryk Wolski http://r4proteomics.sourceforge.net [e-mail]

References

http://www.hgmp.mrc.ac.uk/Software/EMBOSS/overview.html

wolski/pairseqsim documentation built on May 4, 2019, 9:47 a.m.