README.md

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

proxysnps

proxysnps is an R package that implements functions to get proxy SNPs in linkage disequilibrium (LD) with a SNP in the 1000 Genomes Project.

library(proxysnps)
d <- get_proxies(query = "rs42")
plot(d$POS, d$R.squared, main="rs42", xlab="Position", ylab=bquote("R"^2))

Usage

See the vignette for more usage examples.

Installation

install.packages("devtools")
devtools::install_github("slowkow/proxysnps")

Data

This package provides easy access to 1000 Genomes Project VCF files that have been filtered by Brian Browning, available here.

Contributing

Please submit an issue to report bugs or ask questions.

Please contribute bug fixes or new features with a pull request to this repository.

Related work

HaploReg

HaploReg is a tool for exploring annotations of the noncoding genome at variants on haplotype blocks, such as candidate regulatory SNPs at disease-associated loci. Using LD information from the 1000 Genomes Project, linked SNPs and small indels can be visualized along with chromatin state and protein binding annotation from the Roadmap Epigenomics and ENCODE projects, sequence conservation across mammals, the effect of SNPs on regulatory motifs, and the effect of SNPs on expression from eQTL studies.

LDheatmap

Produces a graphical display, as a heat map, of measures of pairwise linkage disequilibria between SNPs. Users may optionally include the physical locations or genetic map distances of each SNP on the plot.

Also see the Statistical Genetics CRAN Task View for additional R packages.

LocusZoom

LocusZoom is a tool to plot regional association results from genome-wide association scans or candidate gene studies.

SNAP

SNAP is a computer program and web-based service for the rapid retrieval of linkage disequilibrium proxy SNP results given input of one or more query SNPs and based on empirical observations from the International HapMap Project and the 1000 Genomes Project.

SNPsnap

The SNPsnap Web server enables SNP-based enrichment analysis by providing matched sets of SNPs that can be used to calibrate background expectations. Specifically, SNPsnap efficiently identifies sets of randomly drawn SNPs that are matched to a set of query SNPs based on allele frequency, number of SNPs in LD, distance to nearest gene and gene density.

Tagger

Tagger is a tool for the selection and evaluation of tag SNPs from genotype data such as that from the International HapMap Project. It combines the simplicity of pairwise tagging methods with the efficiency benefits of multimarker haplotype approaches.

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