In GregoryMatesi/RHiddenAncestries: Hidden Ancestries Group R Package

The R package for estimating ancestry proportions in heterogeneous genetic data. This method was developed by the Hidden Ancestries team at the University of Colorado Denver and is headed by Dr Audrey Hendricks.

Usage

ancestr(D=NULL,k=NULL,t=0)

Arguments

data Dataframe with N SNPs. Variables include Chromosome, RSID, A1, A2, reference ancestry allele frequencies, and one or multiple heterogeneous ancestry allele frequencies.

k Column names of the reference ancestries to be included in the model. Contained in an array of character strings.

t Column name of the heterogeneous observed ancestry as a character string

x0

Details

Value

par k optimal ancestry proportion estimates

val objective function value of the optimal point

iter iterations to achieve optimum

time run time.

filteredNA Amount of NAs removed from the data.

Note

References

See Also

Examples

library(RHiddenAncestries)
# load the data
data(ancestryData)

# Estimate 5 reference ancestry proportion values for the gnomAD african ancestry group
# using a starting guess of .2 for each ancestry proportion.
ancestr( ancestryData, k=c("ref_AF_afr_1000G", "ref_AF_eur_1000G", "ref_AF_sas_1000G", "ref_AF_iam_1000G", "ref_AF_eas_1000G"), t="gnomAD_AF_afr", 
                          x0 = c(.2, .2, .2, .2, .2) )

GregoryMatesi/RHiddenAncestries documentation built on July 9, 2020, 7:58 a.m.