get_proxies: Get proxy SNPs for a SNP at a given genomic position.

In slowkow/proxysnps: Get proxy SNPs for a SNP in the 1000 Genomes Project

Description

Returns a dataframe with proxy SNPs.

Usage

get_proxies(chrom = NA, pos = NA, query = NA, window_size = 1e+05,
  pop = NA)

Arguments

chrom	a chromosome name (1-22,X) without "chr"
pos	a positive integer indicating the position of a SNP
window_size	a positive integer indicating the size of the window
pop	the name of a 1000 Genomes population (AMR,AFR,ASN,EUR,...). Set this to NA to use all populations.

Details

Currently, this is hard-coded to access 1000 Genomes phase3 data hosted by Brian Browning (author of BEAGLE):

http://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes_phase3_v5a/

This implementation discards multi-allelic markers that have a "," in the ALT column.

The pop can be any of: ACB, ASW, BEB, CDX, CEU, CHB, CHS, CLM, ESN, FIN, GBR, GIH, GWD, IBS, ITU, JPT, KHV, LWK, MSL, MXL, PEL, PJL, PUR, STU, TSI, YRI. It can also be any super-population: AFR, AMR, EAS, EUR, SAS.

Find more details here: http://www.1000genomes.org/faq/which-populations-are-part-your-study

Value

A dataframe with the following columns:

CHROM

Chromosome name, e.g. "1"

POS

Position, e.g. 583090

ID

Identifier, e.g. "rs11063140"

REF

Reference allele, e.g. "A"

ALT

Alternative allele, e.g. "G"

MAF

Minor allele frequency, e.g. 0.1

R.squared

Squared Pearson correlation coefficient, e.g. 1.0

D.prime

D prime value, e.g. 1.0

CHOSEN

Binary indicator set to TRUE for the SNP of interest

Examples

d <- get_proxies(chrom = "12", pos = 583090, window_size = 1e5, pop = "AFR")
head(d)
 

slowkow/proxysnps documentation built on May 30, 2019, 3:06 a.m.