findLDblocks {trio}R Documentation

Identifying LD blocks

Description

Finds LD blocks using the procedure proposed by Gabriel et al. (2002).

Usage

findLDblocks(x, alpha = 0.1, ciLD = c(0.7, 0.98), cuRecomb = 0.9, 
   ratio = 9, alsoOthers = FALSE, iter = 50, snp.in.col = TRUE)

Arguments

x either the output of getLD or a numeric matrix consisting of the integers 0, 1, and 2, where these integers are assumed to be the number of minor alleles that the respective SNPs shows at the respective subject. Missing values are allowed. By default, each column of this matrix represents a SNP, and each row a subject (for details, see snp.in.col). The SNPs must be ordered by their position on the considered chromosome.
alpha numeric value between 0 and 1. For each pair of SNPs, a two-sided 100 * (1 - alpha)% confidence interval of D' is computed, and used to specify pairs of SNPs that are either in strong LD, or show historical evidence of recombination (see ciLD and cuRecomb). All SNP pairs not falling into these two categories are specified as 'Others'.
ciLD numeric vector consisting of two values between 0 and 1. If the lower bound of the confidence interval of D' for a SNP pair is larger than or equal to the first value in ciLD and the upper bound is larger than or equal to the second value, then this pair of SNP is considered to be in strong LD.
cuRecomb numeric value between 0 and 1. If the upper bound of the confidence interval of D' for a SNP pair is smaller than cuRecomb, then this pair of SNP is considered to show evidence of recombination.
ratio numeric value larger than 1. If in a block of SNPs, the ratio of the number of SNP pairs being in strong LD to the number of SNPs showing evidence of recombination is larger than or equal to ratio, then this block will be identified as an LD-block. (Note that Gabriel et al. (2002) use ratio = 19 instead of ratio = 9.) Overlapping blocks are avoided by employing the approach described in Wall and Pritchard (2003).
alsoOthers logical value. Following the description of Wall and Pritchard (2003) the endmarkers of a LD block must be in strong LD. By default (i.e.\ if alsoOthers = FALSE), this condition is used. If alsoOthers = TRUE, the endmarkers can also be categorized as 'Others'.
iter integer specifying the number of iterations used in the computation of D (for details, see getLD). Ignored if x is the output of getLD.
snp.in.col logical specifying 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). Ignored if x is the output of getLD.

Details

The LD-blocks are estimated using the method of Gabriel et al. (2002) as described in Wall and Pritchard (2003), where we use the approximate variance estimates of D' proposed by Zabaleta et al. (1997).

Value

An object of class LDblocks consisting of

ld the output of getLD,
blocks a vector specifying which SNP belongs to which LD-block,
vec.blocks a list in which each entry contains the names of the SNPs belonging to a specific LD-block,
param a list of the input parameters.

Author(s)

Holger Schwender, holger.schwender@udo.edu

References

Gabriel, S.B. et al. (2002). The Structure of Haplotype Blocks in the Human Genome. Science, 296, 2225-2229.

Wall, J.D. and Pritchard J.K. (2003). Assessing the Performance of the Haplotype Block Model of Linkage Disequilibrium. American Journal of Human Genetics, 73, 502-515.

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.LDblocks, getLD

Examples

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

# LD blocks can be identified either by
out <- getLD(mat, addVarN=TRUE)
out2 <- findLDblocks(out)
out2

# or directly by
out3 <- findLDblocks(mat)

# Plot Gabriel's categories with LD blocks for all SNPs.
plot(out3)

# Plot Gabriel's categories starting with SNP 24 and 
# ending with SNP 60.
plot(out3,  start=24, end=60)

# Note that the SNPs ABI.354, ABI.355, and ABI.357
# form a LD-block. But since ABI.354 is not part of
# the plot, and thus the block is only shown partly
# in the plot, the vertical block border is missing.

# Now the same for D', but by using the SNP names
plot(out3, "Dprime", start="ABI.355", end="CRC.45")
## End(Not run)

[Package trio version 1.0.2 Index]