snp.dprime-class {snpMatrix} | R Documentation |
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 deliberate. 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)