Data Cleaning:
-
Filtering GWAS 0.05 results
-
Using variants unfiltered for MAF for PCA and heritability analysis
-
Excluding low frequency variants and genomic PCA
-
Re-trying default merge
-
Troubleshooting missing genotype filtering
-
Generating stats for merged data and extracting data for NIES
-
Fixing WGS ID and merging data
-
Extracting data for variants common in both file sets
-
Generating basic statistics for final genomic data sets
-
Merging genomic data sets
-
Cleaning and preparing genomic data
-
Extracting genomic data exclusive to NIES
-
Extracting common variants from both data sets
-
Adding Conjunctival UVAF to dataset
-
Pearson's correlations on imputed data set
-
MIPCA of Phenotypic Data without LogMAR-with-PH values
-
Multiple PCA Imputation of Quantitative Phenotypic Data - updated
-
Example of data imputation with missMDA
-
Understanding PCA
-
Subsetting relevant phenotypic data
-
Finding outliers in quantitative data
-
Plotting histograms for quantitative phenotypic data