gmdm: Generalized Minimum Distance Matrix

In GMD: Generalized Minimum Distance of distributions

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

GMD documentation built on May 29, 2017, 10:41 a.m.