expandSnpSet {ldblock} | R Documentation

## 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

### 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 )

[Package ldblock version 1.22.1 Index]