expandSnpSet: Given a set of SNP identifiers, use LD to expand the set to...

In ldblock: data structures for linkage disequilibrium measures in populations

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

Details

direct use of elementwise arithmetic comparison

Value

character vector

Note

As of 2015, it appears that locus names are more informative than addresses for determining SNP identity across resources.

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 )

ldblock documentation built on Nov. 8, 2020, 5:33 p.m.