README.md

COVID-19: association between expression and AGE/SEX

Script structure

Pipeline: bash run.sh

download_data.sh: download data from GTEX and Gencode for downstream analysis

Script dependencies include the following R packages:

• dplyr
• data.table
• ggplot2
• sva

Approach I: Perform SVA to learn about the SVs, and test asscoations with AGE and SEX controlling for the SVs

extract_protein_coding_lincRNA_genes.sh: Extract genes that are protein coding or lincRNA
generate_tissue_wise_TPM.R: Generate a matrix of genes by samples for each tissue
SVA_compute_SV.R: Infer about surrogate variables (SVs) using SVA
SVA_followedby_LR.R: Perform association tests controlling for SVs

Rscript SVA_followedby_LR.R ENSG00000130234.10 ACE2
Rscript SVA_followedby_LR.R ENSG00000184012.11 TMPRSS2

Approach II: Test asscoations with AGE and SEX controlling for known confounders

Rscript LR_confounders.R ENSG00000130234.10 ACE2
Rscript LR_confounders.R ENSG00000184012.11 TMPRSS2
	* DTHHRDY  - Death Circumstances
	* SMRIN  - RIN number
	* SMTSISCH - Total Ischemic time
	* SMEXNCRT - Exonic Rate