Caitlin E Carey ce-carey

## r_pheno.py
## UKB Phenotypic Correlation Matrices
##
## Generates a phenotypic correlation matrix for all GWAS'ed
## traits, residualized for all GWAS covariates. Also outputs
## a matrix of pairwise N's.
##
## Created by Caitlin E Carey (ccarey@broadinstitute.org)
##
## Last updated 9/27/2019

## README.md

      
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                Hail PRS code
              
          
    PRS Scoring of the UK Biobank Using Hail

The run_prs.py script slack_utils.py was created to generate polygenic risk scores (PRS) in the UK Biobank (UKB) using Hail 0.2. Currently, I have hard-coded the file locations in-line with my own file structure and that of the Neale Lab UKB Round 2 GWAS.
NOTE: This is under active development and generally intended for my own use and the use of my collaborators. ADAPT AT YOUR OWN PERIL!!
How to Run


This script assumes that you have generated an input file using my process-sumstats and LDPred repos.
	## UKB Phenotypic Correlation Matrices
	##
	## Generates a phenotypic correlation matrix for all GWAS'ed
	## traits, residualized for all GWAS covariates. Also outputs
	## a matrix of pairwise N's.
	##
	## Created by Caitlin E Carey (ccarey@broadinstitute.org)
	##
	## Last updated 9/27/2019