LD {GeneticsBase}R Documentation

Pairwise linkage disequilibrium between genetic markers.

Description

Compute pairwise linkage disequilibrium between genetic markers

Usage

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, ...)

Arguments

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

Details

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:

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.

Value

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'

Author(s)

Gregory R. Warnes warnes@bst.rochester.edu

See Also

geneSet-class, diseq

Examples


data(CAMP)

ld <- LD(CAMP)
print(ld)

ldb <- LDband(CAMP)
print(ldb)

ldd <- LDdist(CAMP, posVec=1:8, maxDist=3)
print(ldd)


[Package GeneticsBase version 1.2.0 Index]