Ancestry-specific allele frequency estimates computed by applying ASAFE's EM algorithm to simulated unphased genotypes (ignoring phase information from simulated phased genotypes) and simulated phased ancestries.
A 56,003 x 4 matrix with the following rows, columns, and entries:
Rows: 1 row per bi-allelic marker, with alleles arbitrarily labeled 0 and 1
Columns: Marker ID, followed by ancestries 0, 1, and then 2
Entries: The (i,j)-th entry when j is a column corresponding to an ancestry, gives the estimated frequency of allele 1 amongst admixed chromosomes of that ancestral origin at the i-th marker.
This is the result of applying ASAFE functions to simulated genotype and ancestry data. See ASAFE vignette for details.
Zhang QS, Browning BL, and Browning SR (2016) ”Ancestry Specific Allele Frequency Estimation.” Bioinformatics.
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