Description Usage Arguments Details Value Author(s) References See Also Examples
Finds LD blocks using the procedure proposed by Gabriel et al. (2002).
1 2 3 4 5  findLDblocks(x, alpha = 0.1, ciLD = c(0.7, 0.98), cuRecomb = 0.9,
ratio = 9, alsoOthers = FALSE, parentsOnly = FALSE, iter = 50,
snp.in.col = TRUE)
splitBlocks(blocks)

x 
either the output of 
alpha 
numeric value between 0 and 1. For each pair of SNPs, a twosided
100 * (1  
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 
cuRecomb 
numeric value between 0 and 1. If the upper bound of the confidence
interval of D' for a SNP pair is smaller than 
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 
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 
parentsOnly 
logical indicating whether only the genotypes of the parents, i.e.\ rows 1, 2,
4, 5, ... of 
iter 
integer specifying the number of iterations used in the computation of D (for details,
see 
snp.in.col 
logical specifying whether each column of 
blocks 
output of 
The LDblocks 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).
Since in trio.prepare
the LD blocks are restricted to a maximum of 7 SNPs, splitBlocks
can be used to split LD blocks composed of more than 7 SNPs into smaller blocks, if the output of findLDblocks
should be used in trio.prepare
to prepare a matrix for a trioLR
or trioFS
analysis.
An object of class LDblocks
consisting of

the output of 

a vector specifying which SNP belongs to which LDblock, 

a list in which each entry contains the names of the SNPs belonging to a specific LDblock, 

a list of the input parameters. 
Holger Schwender, holger.schwender@udo.edu
Gabriel, S.B. et al. (2002). The Structure of Haplotype Blocks in the Human Genome. Science, 296, 22252229.
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, 502515.
Zapata, C., Alvarez, G., and Carollo, C. (1997). Approximate Variance of the Standardized Measure of Gametic Disequilibrium D'. American Journal of Human Genetics, 61, 771774.
1 2 3 4 5 6 7 8 9  # Load the simulated data.
data(trio.data)
# Estimate LD blocks.
blocks < findLDblocks(LDdata)
# Alternatively, the LD blocks can be estimated by
ld.out < getLD(LDdata, addVarN=TRUE)
blocks2 < findLDblocks(ld.out)

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