## ----eval=FALSE---------------------------------------------------------------
#  if(!requireNamespace("BiocManager", quietly = TRUE))
#      install.packages("BiocManager")
#  BiocManager::install("Summix")
#  
#  if(!requireNamespace("Summix")){
#      BiocManager::install("Summix")
#  }
#  suppressPackageStartupMessages(library(Summix))

## -----------------------------------------------------------------------------
library("Summix")
# load the data
data("ancestryData")
 
# Estimate 5 reference ancestry proportion values for the gnomAD African/African Amercian ancestry group
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" )

## -----------------------------------------------------------------------------
library("Summix")
# load the data
data("ancestryData")
 
# Estimate 5 reference ancestry proportion values for the gnomAD African/African Amercian ancestry group
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(0.8, 0.1, 0.05, 0.02, 0.03))

## -----------------------------------------------------------------------------
library("Summix")
data(ancestryData)

head(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,]

## ----sessionInfo--------------------------------------------------------------
sessionInfo()