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predixmod's Introduction

###PrediXmod ###Pipeline to develop prediction models for GTEX data and cross-validation

-Instructions for downloading expression and genotype data from GTEx exchange area are listed in gtex.md

-Descriptions of scripts that execute steps in gene prediction model development pipeline shown below:

Convert GTEx genotypes to downstream file formats

  • for all autosomal SNPs combined in one file: 1_vcf2dosage.mach_gtex_hapmapSNPs.pl
  • for separate files per autosome: 1_vcf2dosage.mach.chr_gtex_hapmapSNPs.pl

Convert GTEx RNA-seq data for downstream analyses

  • 2_pull_protein_coding_RPKM_rebuild.pl

Normalize and adjust the GTEx RNA-seq data by PEER factors and genotype principal components

  • 3_calc_PEER_adj_exp.r

Run LASSO cross-validation for GTEx tissue of interest, save R2 and best betas

  • 4_CV_GTEx_lasso_adjusted.r

Run polyscore cross-validation for GTEx tissue of interest, save R2 and top betas

  • 8_CV_GTEX_polyscore_adjusted.r

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