Description Objects from the Class Slots Methods Author(s) See Also Examples

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

.

`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`log2`

s 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

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

Andrew White

1 2 3 4 5 6 7 8 9 10 11 12 13 | ```
#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)
``` |

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