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Estimate ancestry composition from allele frequencies

ancestry_comp.Rd

This function implements the bigsnpr::snp_ancestry_summary() written by Florian Prive.

Usage

ancestry_comp(tbl, dbsnp_path, min_cor = 0.4, sum_to_one = TRUE)

Arguments

tbl

a data.frame with atleast columns RSID, EffectAllele, OtherAllele, and EAF.

dbsnp_path

filepath to the dbSNP reference data. Same path as for tidyGWAS()

min_cor

minimum correlation between predicted and observed allele frequencies.

sum_to_one

Force ancestry coefficients to sum to 1?

Value

a tibble with columns est and ancestry

Details

The function and reference data is based on https://doi.org/10.1093/bioinformatics/btac348

ancestry_comp() requires additional reference data. This data is only available if you have downloaded the updated reference tidyGWAS data The reference file ancestry_data.parquet is expected to exist in the same dbSNP folder that is used with tidyGWAS()

Examples

if (FALSE) { # \dontrun{
ancestry_comp(tbl, "path_to_data")

} # }