snp.dprime-class {chopsticks} | R Documentation

## Class "snp.dprime" for Results of LD calculation

### Description

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.

### Value

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).

### Methods

See `plot.snp.dprime`.

### Note

TODO: Need a subsetting operator.

TODO: an assemble operator

### Author(s)

Hin-Tak Leung htl10@users.sourceforge.net

### Source

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

### References

~~ possibly secondary sources and usages ~~

### Examples

    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)

[Package chopsticks version 1.60.0 Index]