distanceMatrix {ClassDiscovery} | R Documentation |

## Distance Matrix Computation

### Description

This function computes and returns the distance matrix determined by
using the specified distance metric to compute the distances between
the columns fo a data matrix.

### Usage

distanceMatrix(dataset, metric, ...)

### Arguments

`dataset` |
A numeric matrix or an `ExpressionSet` |

`metric` |
A character string defining the distance metric. This
can be `pearson` , `sqrt pearson` , `spearman` ,
`absolute pearson` , `weird` or any of the metrics accepted by the
`dist` function. At present, the latter function accepts
`euclidean` , `maximum` , `manhattan` , `canberra` ,
`binary` , or `minkowski` . Any initial substring that uniquely
defines one of the metrics will work. |

`...` |
Additional parameters to be passed on to
`dist` . |

### Details

This function differs from `dist`

in two ways, both of
which are motivated by common practice in the analysis of microarray
or proteomics data. First, it computes distances between column vectors
instead of between row vectors. In a typical microarray experiment,
the data is organized so the rows represent genes and the columns
represent different biological samples. In many applications,
relations between the biological samples are more interesting than
relationships between genes. Second, `distanceMatrix`

adds
additional distance metrics based on correlation.

`pearson`

- The most common metric used in the microarray literature is
the
`pearson`

distance, which can be computed in terms of the
Pearson correlation coefficient as `(1-cor(dataset))/2`

.
`spearman`

- The
`spearman`

metric used the same formula, but
substitutes the Spearman rank correlation for the Pearson
correlation.
`absolute pearson`

- The
`absolute pearson`

metric used the absolute
correlation coefficient; i.e., `(1-abs(cor(dataset)))`

.
`sqrt pearson`

- The
`sqrt pearson`

metric used the square root of the
pearson distance metric; i.e., `sqrt(1-cor(dataset))`

.
`weird`

- The
`weird`

metric uses the Euclidean distance between
the vectors of correlation coefficients; i.e., dist(cor(dataset)).

### Value

A distance matrix in the form of an object of class `dist`

, of
the sort returned by the `dist`

function or the `as.dist`

function.

### BUGS

It would be good to have a better name for the `weird`

metric.

### Author(s)

Kevin R. Coombes <kcoombes@mdanderson.org>

### See Also

`dist`

, `as.dist`

### Examples

dd <- matrix(rnorm(100*5, rnorm(100)), nrow=100, ncol=5)
distanceMatrix(dd, 'pearson')
distanceMatrix(dd, 'euclid')
distanceMatrix(dd, 'sqrt')
distanceMatrix(dd, 'weird')
rm(dd) # cleanup

[Package

*ClassDiscovery* version 2.5.0

Index]