function to calculate the LD measures of specific SNPs against other SNPs

Description

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

Usage

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

Arguments

Details

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

Value

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.

Warning

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).

Note

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.

Author(s)

Hin-Tak Leung htl10@users.sourceforge.net

See Also

ld.snp, snp.dprime-class

Examples

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))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(chopsticks)
Loading required package: survival
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/chopsticks/ld.with.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ld.with
> ### Title: function to calculate the LD measures of specific SNPs against
> ###   other SNPs
> ### Aliases: ld.with ld.with,snp.matrix,character-method
> ### Keywords: dplot manip models
> 
> ### ** Examples
> 
> data(testdata)
> snps10 <- Autosomes[1:10,1:10]
> obj.snp.dprime <- ld.snp(snps10)
Information: The input contains 10 samples with 10 snps
... Done
> 
> # 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))
Information: The input contains 10 samples with 10 snps
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>