ldblock (version 1.2.2)

expandSnpSet: Given a set of SNP identifiers, use LD to expand the set to include linked loci

Description

Given a set of SNP identifiers, use LD to expand the set to include linked loci

Usage

expandSnpSet(rsl, lb = 0.8, ldstruct, chrn = "chr17", popn = "CEU", 
   txtgzfn = dir(system.file("hapmap", package = "ldblock"), full.names = TRUE))

Arguments

rsl

input list -- SNPs not found in the LD structure are simply returned along with those found, and the expansion list, all combined in a vector

lb

lower bound on statistic used to retrieve loci in LD

ldstruct

instance of ldstruct-class

chrn

chromosome identifier

popn

population identifier (one of 'CEU', 'MEX', ...)

txtgzfn

path to gzipped hapmap file with LD information

Value

• character vector

Details

direct use of elementwise arithmetic comparison

Examples

og = Sys.getenv("LDBLOCK_TXTGZ_DIR")
  on.exit( Sys.setenv("LDBLOCK_TXTGZ_DIR" = og ) )
  Sys.setenv("LDBLOCK_TXTGZ_DIR"=system.file("hapmap", package="ldblock"))
  ld17 = hmld(chr="chr17", pop="CEU")
  ee = expandSnpSet( ld17@allrs[1:10], ldstruct = ld17 )