gmdp: Generalized Minimum Distance between a pair of distributions
In GMD: Generalized Minimum Distance of distributions

Description Usage Arguments Details Value References See Also Examples

Generalized Minimum Distance between a pair of distributions

gmdp(v1, v2, labels=c("v1","v2"), pseudocount=0, sliding=TRUE,
resolution=1)

## S3 method for class 'gmdp'
print(x, mode=c("brief","detailed","full"),
digits=3, ...)

## S3 method for class 'gmdp'
summary(object, ...)

`v1`	a numeric vector, giving positional counts as a discrete distribution.
`v2`	a numeric vector, giving positional counts as a discrete distribution.
`labels`	a string vector of length 2, giving the names of v1 and v2 respectively.
`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.
`x`	an object of class `gmdp`.
`object`	an object of class `gmdp`.
`mode`	a string of the following: `c("brief","detailed","full")`, indicating whether to print in full mode (default).
`digits`	integer, indicating the number of decimal places to be printed.
`...`	arguments to be passed to method.

Generalized Minimum Distance between a pair of distributions

gmdp returns an object of class gmdp, a numeric with an attribute of meta in a list with components:

labels: a string vector, giving the names of distributions

v1.ori: a numeric vector, the first input distribution

v2.ori: a numeric vector, the second input distribution

v1: a numeric vector, the normalized version of the first input distribution

v2: a numeric vector, the normalized version of the second input distribution

distance: numeric, the GM-Distance (GMD)

sliding: logical, indicating whether sliding is performed

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

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

n.hit: numeric, the number of (equally good) optimal hits

See citation("GMD")

print.gmdp, summary.gmdp, plot.gmdp gmdm

require(GMD)
gmdp(c(4,1,1,0,0,0,3,1),c(2,1,1,0,0,0,3,3),sliding=FALSE)
x <- gmdp(c(4,1,1,0,0,0,3,1), c(1,1,2,1,1,0,0,0,3,3,5,5),
pseudocount=1, sliding=TRUE)
print(x)
print(x, "full")