peplib (version 1.03)

MetricParams-class: Class "MetricParams"

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).

Methods

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

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)