ld.with: function to calculate the LD measures of specific SNPs...
In chopsticks: The 'snp.matrix' and 'X.snp.matrix' Classes

Description Usage Arguments Details Value Warning Note Author(s) See Also Examples

This function calculates the LD measures ($r^2$, D', LOD) of specific SNPs against other SNPs.

1	ld.with(data, snps, include.itself = as.logical(length(snps) - 1), signed.r = NULL)

`data`	either a `snp.dprime-class` object or a `snp.matrix-class` object
`snps`	A list of snps, some of which are found in `data`
`include.itself`	Whether to include LD measures of SNPs against itself - it is FALSE for one SNP, since in that case, the result is known and trivial; but otherwise TRUE
`signed.r`	Logical, whether to output signed r or $r^2$

Not all combinations of the include.itself and signed.r make sense, nor fully operational.

The returned value is somewhat similiar to a snp.dprime object, but not the same. It is a list of 3 named matrices dprime, rsq2 (or r depending on the input), lod.

Because this is really two functions rolled into one, depending on the class of data, not all combinations of the include.itself and signed.r make sense, nor fully operational.

Also, the two versions have slightly different idea about invalid values, e.g. the LOD value for a SNPs against itself, or $r^2$ for two monomorphic snps (such as one against itself).

The ld.with function started its life as an extractor function to take the output of ld.snp, a snp.dprime-class object, to rearrange it in a more convenient form to focus on the LD's against specific SNPs, but then evolved to take a snp.matrix-class object alternatively and perform the same task directly and more efficiently.

Hin-Tak Leung htl10@users.sourceforge.net

ld.snp, snp.dprime-class

data(testdata)
snps10 <- Autosomes[1:10,1:10]
obj.snp.dprime <- ld.snp(snps10)

# result1 and result2 should be almost identical
# except where noted in the warning section above:
result1 <- ld.with(obj.snp.dprime, colnames(snps10))
result2 <- ld.with(snps10, colnames(snps10))