summix {Summix}R Documentation

Summix: estimating mixture proportions of reference group

Description

Summix: estimating mixture proportions of reference groups from large (N SNPs>10,000) genetic AF data

Usage

summix(data, reference, observed, pi.start = c())

Arguments

data

a dataframe of the observed and reference allele frequencies for N genetic variants. See data formatting document at https://github.com/hendriau/Summix for more information.

reference

a character vector of the column names for the reference ancestries.

observed

a character value that is the column name for the observed group.

pi.start

length K numeric vector of the starting guess for the ancestry proportions. If not specified, this defaults to 1/K where K is the number of reference ancestry groups.

Value

data frame with the following columns

objective: least square value at solution

iterations: number of iterations for SLSQP algorithm

time: time in seconds of SLSQP algorithm

filtered: number of SNPs not used in estimation due to missing values

K columns of mixture proportions of reference ancestry groups input into the function

Author(s)

Gregory Matesi, gregory.matesi@ucdenver.edu

Audrey Hendricks, audrey.hendricks@ucdenver.edu

See Also

adjAF for adjusting allele frequencies and https://github.com/hendriau/Summix for further documentation. slsqp function in the nloptr package for further details on Sequential Quadratic Programming https://www.rdocumentation.org/packages/nloptr/versions/1.2.2.2/topics/slsqp

Examples

# load the data
data("ancestryData")

# Estimate 5 reference ancestry proportion values for the gnomAD African/African American group
# using a starting guess of .2 for each ancestry proportion.
summix( data = ancestryData, 
    reference=c("ref_AF_afr_1000G", 
        "ref_AF_eur_1000G", 
        "ref_AF_sas_1000G", 
        "ref_AF_iam_1000G", 
        "ref_AF_eas_1000G"), 
    observed="gnomad_AF_afr", 
    pi.start = c(.2, .2, .2, .2, .2) )


[Package Summix version 1.99.2 Index]