LDmatrix | R Documentation |
Generates a data frame of pairwise linkage disequilibrium statistics.
LDmatrix( snps, pop = "CEU", r2d = "r2", token = NULL, file = FALSE, genome_build = "grch37", api_root = "https://ldlink.nci.nih.gov/LDlinkRest" )
snps |
list of between 2 - 1,000 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" |
r2d |
r2d, either "r2" for LD R2 or "d" for LD D', default = "r2" |
token |
LDlink provided user token, default = NULL, register for token at https://ldlink.nci.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. |
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). |
api_root |
Optional alternative root url for API. |
a data frame
## Not run: LDmatrix(c("rs3", "rs4", "rs148890987"), "YRI", "r2", token = Sys.getenv("LDLINK_TOKEN")) ## End(Not run)
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