## ----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()