R: Calculating Linkage Disequilibrium (LD) in Human Population Groups of Interest

# Calculating Linkage Disequilibrium (LD) in Human Population Groups of Interest

## Documentation for package ‘LDlinkR’ version 1.4.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

LDexpress | Determine if genomic variants are associated with gene expression.
LDhap | Calculates population specific haplotype frequencies of all haplotypes observed for a list of query variants.
LDmatrix | Generates a data frame of pairwise linkage disequilibrium statistics.
LDpair | Investigates potentially correlated alleles for a pair of variants.
LDpop | Investigates allele frequencies and linkage disequilibrium patterns across 1000 Genomes Project populations.
LDproxy | Explore proxy and putative functional variants for a single query variant.
LDproxy_batch | Query LDproxy using a list of query variants, one per line.
LDtrait | Determine if genomic variants are associated with a trait or disease.
list_chips | Provides a data frame listing the names and abbreviation codes for available commercial SNP Chip Arrays from Illumina and Affymetrix.
list_gtex_tissues | Provides a data frame listing the GTEx full names, 'LDexpress' full names (without spaces) and acceptable abbreviation codes of the 54 non-diseased tissue sites collected for the GTEx Portal and used as input for the 'LDexpress' function.
list_pop | Provides a data frame listing the available reference populations from the 1000 Genomes Project.
SNPchip | Find commercial genotyping chip arrays for variants of interest.
SNPclip | Prune a list of variants by linkage disequilibrium.