LDexpress: Determine if genomic variants are associated with gene...

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

Determine if genomic variants are associated with gene expression.

Description

Search if a list of genomic variants (or variants in LD with those variants) is associated with gene expression in tissues of interest. Quantitative trait loci data is downloaded from the GTEx Portal (https://gtexportal.org/home/).

Usage

LDexpress(
  snps,
  pop = "CEU",
  tissue = "ALL",
  r2d = "r2",
  r2d_threshold = 0.1,
  p_threshold = 0.1,
  win_size = 5e+05,
  genome_build = "grch37",
  token = NULL,
  file = FALSE,
  api_root = "https://ldlink.nih.gov/LDlinkRest"
)

Arguments

snps	between 1 - 10 variants, using an rsID or chromosome coordinate (e.g. "chr7:24966446")
pop	a 1000 Genomes Project population, (e.g. YRI or CEU), multiple allowed, default = "CEU". Use the 'list_pop' function to see a list of available human reference populations.
tissue	select from 1 - 54 non-diseased tissue sites collected for the GTEx project, multiple allowed. Acceptable user input is taken either from "tissue_name_ldexpress" or "tissue_abbrev_ldexpress" (tissue abbreviation) code listed in available GTEx tissue sites using the list_getex_tissues() function (e.g. "ADI_SUB" for Adipose Subcutaneous). Input is case sensitive. Default = "ALL" for all available tissue types.
r2d	either "r2" for LD R2 or "d" for LD D', default = "r2".
r2d_threshold	R2 or D' (depends on 'r2d' user input parameter) threshold for LD filtering. Any variants within -/+ of the specified genomic window and R^2 or D' less than the threshold will be removed. Value needs to be in the range 0 to 1. Default value is 0.1.
p_threshold	define the eQTL significance threshold used for returning query results. Default value is 0.1 which returns all GTEx eQTL associations with P-value less than 0.1.
win_size	set genomic window size for LD calculation. Specify a value greater than or equal to zero and less than or equal to 1,000,000 basepairs (bp). Default value is -/+ 500,000bp.
genome_build	Choose between one of the three options...'grch37' for genome build GRCh37 (hg19), 'grch38' for GRCh38 (hg38), or 'grch38_high_coverage' for GRCh38 High Coverage (hg38) 1000 Genome Project data sets. Default is GRCh37 (hg19).
token	LDlink provided user token, default = NULL, register for token at https://ldlink.nih.gov/?tab=apiaccess
file	Optional character string naming a path and file for saving results. If file = FALSE, no file will be generated, default = FALSE.
api_root	Optional alternative root url for API.

Value

A data frame of all query variant RS numbers, respective QTL which are in LD with query variant, and associated gene expression.

Examples

## Not run: LDexpress(snps = c("rs345", "rs456"),
                   pop = c("YRI", "CEU"),
                   tissue = c("ADI_SUB", "ADI_VIS_OME"),
                   r2d = "r2",
                   r2d_threshold = "0.1",
                   p_threshold = "0.1",
                   win_size = "500000",
                   genome_build = "grch37",
                   token = Sys.getenv("LDLINK_TOKEN")
                  )
         
## End(Not run)

LDlinkR documentation built on May 29, 2024, 4:32 a.m.