LD {GeneticsBase} | R Documentation |
Compute pairwise linkage disequilibrium between genetic markers
LD(object, ...) LDband(object, width=31,founderOnly=FALSE,...) LDband.geneSet(object,width=31, founderOnly=FALSE) LDdist.geneSet(object,posVec, maxDist, founderOnly=FALSE) summary.LD(object, which = c("D", "D'", "r", "R^2", "X^2", "P-value", "LOD", "n"), rowsep, digits = 3, ...)
object |
geneSet object |
width |
window width |
posVec |
marker position |
maxDist |
size of the window based on distance |
which |
character string indicates which LD statistic should be print out |
rowsep |
separator for rows |
digits |
the desired number of digits after the decimal point |
founderOnly |
Indicates if only founders are used to do the test. |
... |
additional optional arguments |
Linkage disequilibrium (LD) is the non-random association of marker alleles and can arise from marker proximity or from selection bias.
LD
estimates the extent of LD for all pairs of
genotypes contained in a object
. LDband
computes the
extent of LD of markers within a window containing
width
markers centered around each marker in object
.
The current (temporary) code only computes LD for markers with exactly
2 variants. For other markers, NA
is returned.
Three estimators of LD are computed:
D = p(AB) - p(A)*p(B)
D' = D / Dmax
where, if D > 0:
Dmax = min( p(A)p(b), p(a)p(B) )
or if D < 0:
Dmax = max( -p(A)p(B), -p(a)p(b) )
r = -D / sqrt( p(A) * p(a) * p(B) * p(b) )
where
For genotype data, AB/ab cannot be distinguished from aB/Ab. Consequently, we estimate p(AB) using maximum likelihood and use this value in the computations.
LD
returns an object of class LD
, while LDband
and LDdist
return objects of classes LDband
and LDdist
,
respectively. All classes contain these
slots:
call |
the matched call |
D |
Linkage disequilibrium estimate |
Dprime |
Scaled linkage disequilibrium estimate |
corr |
Correlation coefficient |
nobs |
Number of observations |
chisq |
Chi-square statistic for linkage equilibrium (i.e., D=D'=corr=0) |
p.value |
Chi-square p-value for marker independence |
LOD |
LOD scores |
tab |
Description of 'tab' |
statlist |
Description of 'statlist' |
which |
Description of 'which' |
object |
Description of 'object' |
Gregory R. Warnes warnes@bst.rochester.edu
data(CAMP) ld <- LD(CAMP) print(ld) ldb <- LDband(CAMP) print(ldb) ldd <- LDdist(CAMP, posVec=1:8, maxDist=3) print(ldd)