getLD {trio}R Documentation

Computation of LD Measures

Description

Computes the value of D' and r^2 for each pair of SNPs in a matrix.

Usage

  getLD(x, which = c("both", "rSquare", "Dprime"), iter = 50, 
     snp.in.col = TRUE, asMatrix = FALSE, addVarN = FALSE)

Arguments

x a numeric matrix consisting of 0, 1, and 2, where it is assumed that the values represent the numbers of minor alleles that the SNPs show. Missing values are allowed. By default, each column represents a SNP and each row a subject. This can be changed by setting snp.in.col = FALSE. The SNPs should be ordered by their position on the considered chromosome.
which which LD measures should be computed? Either "rSquare", or "Dprime", or the values of "both" measures are computed. The latter is the default.
iter integer specifying how many iterations are used in the procedure of Hill (1974) which is used to estimate D.
snp.in.col logical indicating whether each column of x represents a SNP (and each row a subject). If FALSE, each row represents a SNP (and each column a subject).
asMatrix logical indicating whether the LD values are returned as a m x m matrix, where m is the number of SNPs. If FALSE, the LD values are returned as a vector of length m * (m - 1) / 2.
addVarN logical indicating whether for each pair of SNPs the number of non-missing values and the variance estimates of D' proposed by Zabaleta et al. (1997) should be added to the output. The variance estimates are required for the identification of LD-blocks with findLDblocks.

Value

An object of class getLD consisting (depending of the specification of which) the D' (Dprime) or r^2 (rSquare) values for each SNP pair, and (depending of the specification of addVarN) the variance estimates for D' (varDprime) and the numbers of non-missing values (n). Furthermore, the names of the SNPs (rn) will be added if asMatrix = FALSE.

Author(s)

Holger Schwender, holger.schwender@udo.edu

References

Hill, W.O. (1974). Estimation of Linkage Disequilibrium in Randomly Mating Populations. Heredity, 33, 229-239.

Zapata, C., Alvarez, G., and Carollo, C. (1997). Approximate Variance of the Standardized Measure of Gametic Disequilibrium D'. American Journal of Human Genetics, 61, 771-774.

See Also

plot.getLD, findLDblocks

Examples

## Not run: 
# Andrea's data
data(mat)

out <- getLD(mat, addVarN=TRUE)

# Plot r^2
plot(out)

# Plot r starting with SNP 24 and ending with SNP 60.
plot(out, squared=FALSE, start=24, end=60)

# Now the same for D'.
plot(out, "Dprime", start=24, end=60)

# Now Gabriel's categories starting with SNP ABI.355
# and ending with SNP CRC.45.
plot(out, "gabriel", start="ABI.355", end="CRC.45")
## End(Not run)

[Package trio version 1.0.2 Index]