Nothing
## ---- eval=FALSE---------------------------------------------------------
# $plink --bfile All-00
# --bmerge Prep.bed Prep.bim Prep.fam
# --make-bed --out PrepMerge
## ---- eval=FALSE---------------------------------------------------------
# $plink --bfile Prep --flip PrepMerge-merge.missnp --make-bed --out PrepFlipped
#
# $plink --bfile All-00
# --bmerge PrepFlipped.bed PrepFlipped.bim PrepFlipped.fam
# --make-bed --out PrepMerge
## ---- eval=FALSE---------------------------------------------------------
# $plink --bfile PrepMerge --remove IndRm --make-bed --out PrepMerge
## ---- eval=FALSE---------------------------------------------------------
# $plink --bfile PrepMerge --transpose --recode --write-snplist --out PrepFinal
## ---- eval=FALSE---------------------------------------------------------
# library(AncestryMapper)
#
# #Path to folder containing population references
# Refs <- system.file('data', package = 'AncestryMapper')
#
# #Path to folder containing samples in tPED format
# tpeds <- system.file('extdata', package = 'AncestryMapper')
#
# #Path to CorPheno file
# Corpheno <- system.file('extdata', 'CorPheno', package = 'AncestryMapper')
#
# #Path to dbSNP allele data file
# All00Frq <- system.file('data', 'MinMaxFreq.rda', package = 'AncestryMapper')
#
## ---- eval=FALSE---------------------------------------------------------
# genetic.distance <- calculateAMidsArith(pathTotpeds = tpeds,
# NameOut = 'Example',
# pathToAriMedoids = Refs,
# pathAll00 = All00Frq)
## ---- eval=FALSE---------------------------------------------------------
# plotAMids(AMids = genetic.distance, phenoFile = Corpheno, columnPlot = 'I')
## ---- eval=FALSE---------------------------------------------------------
# #Path to folder containing samples for each population in tPED format
# tpeds <- system.file("extdata", package = "AncestryMapper")
#
# #Path to dbSNP allele data file
# All00Frq <- system.file("data", "MinMaxFreq.rda", package = "AncestryMapper")
#
# createMedoid(pathTotpeds = tpeds, pathAll00 = All00Frq)
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