Submatrix-class {pairseqsim}R Documentation

Class "Submatrix" Substitution Matrix

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 witek96@users.sourceforge.net

References

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


[Package pairseqsim version 1.0.4 Index]