Runs the zmix preparation and constrained quadratic programming to estimate ancestry proportions at the population or superpopulation level.
Usage
zmix(
input_file,
reference_index_file,
reference_data_file,
reference_pop_desc_file,
percentile = 0.9,
interval = 10,
level = c("population", "superpopulation")
)Arguments
- input_file
File name of input data containing rsid, chr, bp, a1, a2, and z.
- reference_index_file
File name of reference panel index data.
- reference_data_file
File name of reference panel data.
- reference_pop_desc_file
File name of reference panel population description data.
- percentile
Percentile cutoff for normalized variance.
- interval
Interval for selecting SNPs.
- level
Resolution of ancestry proportions: "population" or "superpopulation".