MetricParams-class: Class "MetricParams"

In peplib: Peptide Library Analysis Methods

Description

This class stores the parameters used for calcaulting sequence-sequence distances. The parameters are all based on the use of substitution matrices and scores. For example, the BLOSUM matrices may be used. Three possible matrices can be accessed using a call to data(blosumXX) command to create new parameter sets, where XX is 50, 62, or 90. These metric parameter are passed into a few other methods, see the examples below.

Objects from the Class

Objects can be created by calls of the form new("MetricParams", smatrix=blosumXX, gapOpen=-10, gapExtension=-0.2).

Slots

smatrix:

Object of class "matrix" The substitution matrix, where each element represent the log2 of the probability of mutating to that residue. For example, column 3, row 7 is log2 of the probability of mutating from 3 to 7. However, these probabilities are not normalized correctly; instead substition matrices were designed to have the sum of theirs log2s of the probabilities be negative.

gapOpen:

Object of class "numeric" The penalty score for opening a gap

gapExtension:

Object of class "numeric" The penalty score for extending an exisgting gap

Methods

No methods defined with class "MetricParams" in the signature.

Author(s)

Andrew White

See Also

Sequences the dist method.

Examples

#Load the classic BLOSUM62 matrix
data(blosum62)
#Set slightly different gap open, and gap extend parameters
b62params <- new("MetricParams", smatrix=blosum62, gapOpen=-8,
gapExtension=-5)
data(TULASequences)
plot(TULASequences, params=b62params)

#Change the metric parameters to a more stringent substitution matrix
data(blosum90)
b90 <- new("MetricParams", smatrix=blosum90, gapOpen=-8,
gapExtension=-5)
plot(TULASequences, params=b90)

peplib documentation built on May 29, 2017, 10:52 p.m.