Recent entries:

• Filtering GWAS 0.05 results

  01-08-2019 | tags: [ Data Cleaning GWAS R ] categories: [ Coding ]

• GWAS rerun MAF 0.05

  12-21-2018 | tags: [ Gaston GWAS R ] categories: [ Coding Experiments ]

• Using variants unfiltered for MAF for PCA and heritability analysis

  11-26-2018 | tags: [ Data Cleaning Genomic Data Heritability PCA ] categories: [ Coding Experiments ]

• Re-estimating heritability of traits - GCTA

  11-09-2018 | tags: [ GCTA Heritability ] categories: [ Coding Experiments Reading ]

• Excluding low frequency variants and genomic PCA

  11-07-2018 | tags: [ Data Cleaning PCA PLINK ] categories: [ Coding Experiments ]

• Generating beta-values for significant SNPs

  09-26-2018 | tags: [ Gaston Genomic Data GWAS Heritability ] categories: [ Coding ]

• Filtering GWAS (w/ covariates) results

  09-25-2018 | tags: [ Gaston Genomic Data GWAS Heritability ] categories: [ Coding Experiments ]

• Adding age and sex as covariates

  09-21-2018 | tags: [ Gaston GCTA Genomic Data GREML Heritability ] categories: [ Coding Experiments ]

• SNP heritability

  09-19-2018 | tags: [ Gaston GCTA Genomic Data GWAS Heritability MLMA ] categories: [ Experiments Coding ]

• Annotating signficant GWAS hits

  09-11-2018 | tags: [ Genomic Data GWAS ] categories: [ Coding Experiments ]

• Performing GWAS on heritable traits

  09-07-2018 | tags: [ Gaston GCTA Genomic Data GWAS Heritability ] categories: [ Coding Experiments ]

• MLMA GWAS for most heritable trait

  09-06-2018 | tags: [ GCTA Genomic Data GWAS MLMA GREML Linux ] categories: [ Coding Experiments ]

• Estimating heritability of principal components using GCTA

  09-05-2018 | tags: [ GCTA Genomic Data Heritability ] categories: [ Coding Experiments ]

• Trying GCTA to perform heritability analysis

  09-03-2018 | tags: [ GCTA Genomic Data Heritability Linux ] categories: [ Coding Experiments ]

• Including principal components for estimating heritability

  08-22-2018 | tags: [ Gaston Genomic Data Heritability ] categories: [ Coding Experiments ]

• Using gaston for estimating heritability-1

  08-19-2018 | tags: [ Gaston Genomic Data R PLINK Heritability ] categories: [ Coding Experiments ]

• Trying gaston to generate genetic relationship matrix

  08-16-2018 | tags: [ Genomic Data Gaston ] categories: [ Coding Experiments ]

• Performing PCA on filtered NIES genomic data

  08-14-2018 | tags: [ Genomic Data PCA PLINK ] categories: [ Coding Experiments ]

• Re-trying default merge

  08-14-2018 | tags: [ Data Cleaning Genomic Data PLINK R ] categories: [ Coding Experiments ]

• Troubleshooting missing genotype filtering

  08-11-2018 | tags: [ Data Cleaning Genomic Data PLINK R ] categories: [ Coding Experiments ]

• Performing PCA on genomic data

  08-08-2018 | tags: [ Genomic Data Linux PCA PLINK R ] categories: [ Coding Experiments ]

• Generating stats for merged data and extracting data for NIES

  08-03-2018 | tags: [ Data Cleaning Genomic Data Linux PLINK ] categories: [ Coding Experiments ]

• Fixing WGS ID and merging data

  08-02-2018 | tags: [ Data Cleaning Genomic Data Linux PLINK R ] categories: [ Coding Experiments ]

• Extracting data for variants common in both file sets

  08-01-2018 | tags: [ Data Cleaning Genomic Data Linux PLINK R ] categories: [ Coding Experiments ]

• Generating basic statistics for final genomic data sets

  07-31-2018 | tags: [ Data Cleaning Genomic Data Linux PLINK ] categories: [ Coding Experiments ]

• Converting SNP array data

  07-26-2018 | tags: [ Genomic Data PLINK ] categories: [ Coding Experiments ]

• Merging genomic data sets

  07-25-2018 | tags: [ Data Cleaning Genomic Data Linux PLINK ] categories: [ Coding Experiments ]

• Cleaning and preparing genomic data

  07-24-2018 | tags: [ Data Cleaning Genomic Data Linux PLINK R ] categories: [ Coding Experiments ]

• Extracting genomic data exclusive to NIES

  07-05-2018 | tags: [ Genomic Data Data Cleaning Linux PLINK R ] categories: [ Coding Experiments ]

• Generating basic statistics for merged data set

  07-04-2018 | tags: [ Genomic Data Linux PLINK R ] categories: [ Coding Experiments ]

• Extracting common variants from both data sets

  07-03-2018 | tags: [ Data Cleaning Genomic Data Linux PLINK PCA R ] categories: [ Coding Experiments ]

• Generating basic statistics for genomic data sets

  06-27-2018 | tags: [ Genomic Data Linux PLINK ] categories: [ Coding Experiments ]

• Trying bmerge function

  06-15-2018 | tags: [ Genomic Data Linux PLINK ] categories: [ Coding Experiments ]

• Getting started with PLINK

  06-13-2018 | tags: [ Linux PLINK Genomic Data ] categories: [ Coding ]

• PCA of Phenotypic Data

  05-17-2018 | tags: [ PCA Ocular Biometry R ] categories: [ Coding Experiments ]

• Adding Conjunctival UVAF to dataset

  05-10-2018 | tags: [ Bivariate Correlations Data Cleaning Imputation Ocular Biometry PCA R ] categories: [ Coding Experiments ]

• Pearson's correlations on imputed data set

  05-09-2018 | tags: [ Data Cleaning Imputation Bivariate Correlations R ] categories: [ Coding Experiments ]

• MIPCA of Phenotypic Data without LogMAR-with-PH values

  05-05-2018 | tags: [ Data Cleaning Imputation PCA R ] categories: [ Coding Experiments ]

• Multiple PCA Imputation of Quantitative Phenotypic Data - updated

  05-04-2018 | tags: [ Data Cleaning Imputation PCA R ] categories: [ Coding Experiments ]

• Multiple PCA Imputation of Phenotypic Data

  04-29-2018 | tags: [ R Imputation PCA ] categories: [ Coding Experiments ]

• Example of data imputation with missMDA

  04-23-2018 | tags: [ Data Cleaning Imputation PCA R ] categories: [ Experiments Coding ]

• Understanding PCA

  04-23-2018 | tags: [ PCA Imputation Data Cleaning ] categories: [ Reading ]

• Subsetting relevant phenotypic data

  04-21-2018 | tags: [ Data Cleaning R ] categories: [ Coding ]

• Understanding ocular biometric measurements

  04-20-2018 | tags: [ Reading Ocular Biometry ] categories: [ Reading ]

• Finding outliers in quantitative data

  04-16-2018 | tags: [ Data Cleaning R ] categories: [ Coding Experiments ]

• Plotting histograms for quantitative phenotypic data

  04-10-2018 | tags: [ R Data Cleaning ] categories: [ Coding ]

• Cleaning phenotypic data

  04-05-2018 | tags: [ R ] categories: [ Coding ]