expandByLD: For genotypes identify proxy SNPs (with R2 above threshold)
In IngaPa/myDNA: myDNA: R package to analyze personal genotypes

Description Usage Arguments Details Author(s)

For genotypes identify proxy SNPs (with R2 above threshold)

1	expandByLD(myDNA, pop = "CEU", R.squared = 0.8, chunks = 1, out.dir)

`myDNA`	GRanges object, output of importDNA function
`pop`	(character, default EUR) the name of a 1000 Genomes population (AMR,AFR,ASN,EUR,...). Set this to NA to use all populations.
`R.squared`	(numeric) threshold for R.squared statistics used to assess LD
`chunks`	(numeric, default=1). Enables running function for N chunks of SNPs. It is to intensive to run it on the full set of genotypes (700k) so it is better to split it into cca 1000 chunks
`out.dir`	(character) path to the directory where data will be stored

For analyzed genotypes (myDNA) this function identifies all SNPs that in LD above predefined threshold. Since number of SNPs is large (>700k) analysis is separated into chunks, and results are pooled together in the end In addition, chunks and final results are saved in the out.dir

Inga Patarcic

IngaPa/myDNA documentation built on Oct. 30, 2019, 7:22 p.m.