Individual-level metadata for 1000 Genomes Project (Phase 1).
data("popDat_1KGphase1")
data.table
popDat_URL <- "ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20110521/phase1_integrated_calls.20101123.ALL.panel"
popDat_1KGphase1 <- data.table::fread(text = trimws(gsub(",\t", ",", readLines(popDat_URL))), sep = "\t", fill = T, stringsAsFactors = F, col.names = c("sample", "population", "superpop", "sex"), nThread = 4)
usethis::use_data(popDat_1KGphase1, overwrite = T)
Other LD:
LD_1KG_download_vcf(),
LD_1KG(),
LD_custom(),
LD_ukbiobank(),
compute_LD(),
filter_LD(),
get_locus_vcf_folder(),
ldlinkr_ldproxy_batch(),
load_or_create(),
plot_LD(),
popDat_1KGphase3,
rds_to_npz(),
saveSparse(),
save_LD_matrix(),
snpstats_get_MAF(),
translate_population()