- 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.