LDSearch: Search for SNPs in LD with a set of SNPs

In kevinushey/SNAPR: An R interface to the online LD tool SNAP (SNP Annotation and Proxy Search)

Description

This function queries SNAP for SNPs in high linkage disequilibrium with a set of SNPs.

Usage

  LDSearch(SNPs, dataset = "onekgpilot", panel = "CEU",
    RSquaredLimit = 0.8, distanceLimit = 500,
    GeneCruiser = TRUE)

Arguments

SNPs	A vector of SNPs (rs numbers).
dataset	The dataset to query. Must be one of: rel21: HapMap Release 21 rel22: HapMap Release 22 hapmap3r2: HapMap 3 (release 2) onekgpilot: 1000 Genomes Pilot 1
panel	The panel to use from the queried data set. Must be one of: CEU YRI JPT+CHB If you are working with hapmap3r2, you can choose the additional panels: ASW CHD GIH LWK MEK MKK TSI CEU+TSI JPT+CHB+CHD
RSquaredLimit	The R Squared limit to specify as a filter for returned SNPs; that is, only SNP pairs with R-squared greater than RSquaredLimit will be returned.
distanceLimit	The distance (in kilobases) upstream and downstream to search for SNPs in LD with each set of SNPs.
GeneCruiser	boolean; if TRUE we attempt to get gene info through GeneCruiser for each SNP. This can slow the query down substantially.

Details

For more details, please see http://www.broadinstitute.org/mpg/snap/ldsearch.php.

Information on the HapMap populations: http://ccr.coriell.org/Sections/Collections/NHGRI/hapmap.aspx?PgId=266&coll=HG

Information on the 1000 Genomes populations: http://www.1000genomes.org/category/frequently-asked-questions/population

Value

A list of data frames, one for each SNP queried, containing information about the SNPs found to be in LD with that SNP.

Examples

## Not run: LDSearch("rs420358")

kevinushey/SNAPR documentation built on May 20, 2019, 9:09 a.m.