| 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)