snp.dprime-class: Class "snp.dprime" for Results of LD calculation
In chopsticks: The 'snp.matrix' and 'X.snp.matrix' Classes

Description Value Methods Note Author(s) Source References Examples

The snp.dprime class encapsulates results returned by ld.snp (— routine to calculate D', $r^2$ and LOD of a snp.matrix-class object, given a range and a depth) and is based on a list of three named matrices.

The lower right triangle of the snp.dprime object returned by ld.snp always consists zeros. This is delibrate. The associated plotting routine would not normally access those elements either.

The snp.dprime class is a list of 3 named matrices dprime, rsq2 or r, lod, and an attribute snp.names for the list of snps involved. (Note that if $x$ snps are involved, the row numbers of the 3 matrices are $(x-1)$). Only one of r or rsq2 is present.

`dprime`	D'
`rsq2`	$r^2$
`r`	signed $r^2$
`lod`	Log of Odd's
`attr(*, class)`	"snp.dprime"
`attr(*, snp.names)`	character vectors of the snp names involved

All the matrices are defined such that the ($n, m$)th entry is the pair-wise value between the ($n$)th snp and the $(n+m)$th snp. Hence the lower right triangles are always filled with zeros.

Invalid values are represented by an out-of-range value - currently we use -1 for D', $r^2$ (both of which are between 0 and 1), and -2 for $r$ (valid values are between -1 and +1). lod is set to zero in most of these invalid cases. (lod can be any value so it is not indicative).

See plot.snp.dprime.

TODO: Need a subsetting operator.

TODO: an assemble operator

Hin-Tak Leung htl10@users.sourceforge.net

~~ reference to a publication or URL from which the data were obtained ~~

~~ possibly secondary sources and usages ~~

data(testdata)
snps20.20 <- Autosomes[11:20,11:20]
obj.snp.dprime <- ld.snp(snps20.20)
class(obj.snp.dprime)
summary(obj.snp.dprime)
## Not run: 
# The following isn't executable-as-is example, so these illustrations
# are commented out to stop R CMD check from complaining:

> d<- ld.snp(all, 3, 10, 15) 
rows = 48, cols = 132
... Done
> d
$dprime
     [,1] [,2] [,3]
[1,]    1    1    1
[2,]    1    1    1
[3,]    1    1    1
[4,]    1    1    0
[5,]    1    0    0

$rsq2
          [,1]      [,2]      [,3]
[1,] 1.0000000 0.9323467 1.0000000
[2,] 0.9285714 1.0000000 0.1540670
[3,] 0.9357278 0.1854481 0.9357278
[4,] 0.1694915 1.0000000 0.0000000
[5,] 0.1694915 0.0000000 0.0000000

$lod
          [,1]      [,2]      [,3]
[1,] 16.793677 11.909686 16.407120
[2,] 10.625650 15.117962  2.042668
[3,] 12.589586  2.144780 12.589586
[4,]  2.706318 16.781859  0.000000
[5,]  2.706318  0.000000  0.000000

attr(,"class")
[1] "snp.dprime"
attr(,"snp.names")
[1] "dil118"  "dil119"  "dil5904" "dil121"  "dil5905" "dil5906"


## End(Not run)