adjAF {Summix}R Documentation

Ancestry adjusted allele frequencies

Description

Adjusts allele frequencies for heterogeneous populations in genetic data given proportion of reference ancestry groups

Usage

adjAF(data, reference, observed, pi.target, pi.observed)

Arguments

data

dataframe of unadjusted allele frequency for observed group, K-1 reference ancestry allele frequencies for N SNPs

reference

character vector of the column names for K-1 reference ancestry groups. The name of the last reference ancestry group is not included as that group is not used to estimate the adjusted allele frequencies.

observed

character value for the column name of observed data group

pi.target

numeric vector of the mixture proportions for K reference ancestry groups in the target sample or subject. The order must match the order of the reference columns with the last entry matching the missing reference group.

pi.observed

numeric vector of the mixture proportions for K reference ancestry groups for the observed group. The order must match the order of the reference columns with the last entry matching the missing reference group.

Value

pi: table of input reference ancestry groups, pi.observed, and pi.target

observed.data: name of the data column for the observed group from which adjusted ancestry allele frequency is estimated

Nsnps: number of SNPs for which adjusted AF is estimated

adjusted.AF: data frame of original data with an appended column of adjusted allele frequencies

Author(s)

Gregory Matesi, gregory.matesi@ucdenver.edu

Audrey Hendricks, audrey.hendricks@ucdenver.edu

See Also

summix for estimating the proportion of reference ancestry groups and https://github.com/hendriau/Summix for further documentation

Examples

data(ancestryData)
tmp.aa<-adjAF(data   = ancestryData,
    reference   = c("ref_AF_eur_1000G"),
    observed    = "gnomad_AF_afr",
    pi.target   = c(0, 1),
    pi.observed = c(.15, .85))
tmp.aa$adjusted.AF[1:5,]

[Package Summix version 1.0.3 Index]