genotype files (.ped/.map)
Local ancestry information:
PCAdmix outputsfiles (.bed/.marker/.vit)
per chromosome
admixturemapping_pcadmix2additive012_African.r
admixturemapping_pcadmix2additive012_European.r
admixturemapping_pcadmix2additive012_NativeAmerican.r
.ped/.map files with local ancestry
(--recode12 format) per chromosome
per ancestry
.window file
PLINK (--merge function)
.ped/.map files for all autosomes
per ancestry
PLINK (--recodeA function)
.raw files per ancestry
phenotype information file
(--pheno)
covariates information file
(--covar)
PLINK
logistic (--logistic function) or
linear (--linear function) regression per ancestry
linear or logistic regression
outputs of
PCAdmix windows
Logistic or Linear Regression by
R Scripts per ancestry
Family cluster information file
(for Bambui)
Imputation and Fine mapping
for each associated window
Association Study for imputaded SNPs
of each associated window
Associated SNPs list
SNP annotation
Effective number of tests (ENT) estimation
for each chr for each individual per ancestry:
coda package
ENT for each chromosome
for each individual per ancestry
ENT sum for all chromosome
for each individual per ancestry
ENT per individual
per ancestry
Calculation of ENT average
across individuals per ancestry
ENT average
per ancestry
Bonferroni correction:
0.05/ENT_average
p-value threshold
for significance per ancestry
linear or logistic regression
outputs of
RFMix windows
.raw files per ancestry of
PCAdmix windows
p-value threshold * 5
filtered PCAdmix windows
filtered RFMix windows
compare Windows
Windows are
mapped for the
same regions?
Windows excluded
Consensus windows
2
Definition of p-value threshold
Phenotype associated to
a specific ancestry
Admixed Population
genetic data
PCAdmix and RFMix:
Local Ancestry Inference
Parental Populations
Genetic Data
ADMIXTURE
Individual Ancestry Inference
No
Yes