R: Generalized Minimum Distance Matrix

gmdm {GMD} | R Documentation

## Generalized Minimum Distance Matrix

### Description

Computing Generalized Minimum Distance Matrix

### Usage

    gmdm(data,labels,pseudocount=0,sliding=TRUE,resolution=1)

    ## S3 method for class `gmdm'
    ## S3 method for class 'gmdm'
    print(x, ...)

    ## convert a `gmdm' object into a `dist' object
    gmdm2dist(m, diag=FALSE, upper=FALSE)

    ## compute GMDM and convert into a `dist' object
    gmdm_dist(data, diag=FALSE, upper=FALSE, ...)

### Arguments

`data` | a list of numeric vectors, a numeric matrix or data.frame
`x` | a `gmdm` object.
`m` | a `gmdm` object.
`labels` | a character vector of the same length of x, giving the names of the numeric vectors.
`pseudocount` | a numeric value to be allocated for each position to reduce bias; by default `pseudocount = 0`.
`sliding` | logical, indicating whether sliding is allowed or not for an optimal solution; by default `sliding = TRUE`.
`resolution` | relative resolution, numeric (>=1), changing the size of the bin by multiplying the value. A larger value (lower resolution) is more computational efficiet but missing details.
`diag` | logical value indicating whether the diagonal of the distance matrix should be printed by `print.dist`.
`upper` | logical value indicating whether the upper triangle of the distance matrix should be printed by `print.dist`.
`...` | arguments to be passed to method

### Details

Computing Generalized Minimum Distance Matrix

### Value

`gmdm` returns an object of class `gmdm`, a list with components

labels: a string vector, giving the names of distributions

data.ori: a list of numeric vectors, giving the original input

data: a list of numeric vectors, giving the normalized version of the original input

dm: a numeric numeric, the pairwise distance matrix of GM-Distances

gap.pair: a numeric matrix, giving the gap pair of each alignment per row: i.e. relative shifts between distributions of the optimal hit

sliding: logical, indicating whether sliding is performed

pseudocount: a numeric value that is allocated at each position in addition to original values

### References

See `citation("GMD")`

### See Also

`plot.gmdm`, `gmdp`

[Package GMD version 0.3.3 Index]