Experiments:
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GWAS rerun MAF 0.05
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Using variants unfiltered for MAF for PCA and heritability analysis
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Re-estimating heritability of traits - GCTA
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Excluding low frequency variants and genomic PCA
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Filtering GWAS (w/ covariates) results
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Adding age and sex as covariates
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SNP heritability
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Annotating signficant GWAS hits
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Performing GWAS on heritable traits
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MLMA GWAS for most heritable trait
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Estimating heritability of principal components using GCTA
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Trying GCTA to perform heritability analysis
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Including principal components for estimating heritability
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Using gaston for estimating heritability-1
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Trying gaston to generate genetic relationship matrix
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Performing PCA on filtered NIES genomic data
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Re-trying default merge
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Troubleshooting missing genotype filtering
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Performing PCA on genomic data
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Generating stats for merged data and extracting data for NIES
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Fixing WGS ID and merging data
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Extracting data for variants common in both file sets
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Generating basic statistics for final genomic data sets
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Converting SNP array data
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Merging genomic data sets
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Cleaning and preparing genomic data
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Extracting genomic data exclusive to NIES
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Generating basic statistics for merged data set
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Extracting common variants from both data sets
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Generating basic statistics for genomic data sets
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Trying bmerge function
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PCA of Phenotypic Data
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Adding Conjunctival UVAF to dataset
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Pearson's correlations on imputed data set
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MIPCA of Phenotypic Data without LogMAR-with-PH values
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Multiple PCA Imputation of Quantitative Phenotypic Data - updated
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Multiple PCA Imputation of Phenotypic Data
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Example of data imputation with missMDA
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Finding outliers in quantitative data