An R package to Identify cis-cis epistasis effects on gene expression
This package implements multiple analysis strategies for identifying cis-cis epistasis effects on gene expression for specific genes.
To install:
install.packages("epiEQTL_1.0.tar.gz", repos=NULL, source=TRUE)
To run in R: library(epiEQTL)
geno_file="geno_chr11_pass" expression_file="expression_counts.csv" covariate_file="gene_expression_covariates.txt" subj_select="subject_select.txt" folder = "/udd/redaq/epiRNA/newRcode/Example" GENE = "MUC5B" flank = 1000 design = "~Lc.Batchadapter.test+PC1+PC2+PC3+peer_factor_1+peer_factor_2+peer_factor_3" MAC = "5" missingRate = "0.01" eQTLFile = "cisEQTL.txt" plink2exe="/udd/redaq/tools/plink2" plinkexe="/udd/redaq/tools/plink032819/plink"
results=compute_Epistasis_eQTL(plink2exe, plinkexe,geno_file, expression_file, covariate_file, subj_select, folder, GENE, flank, design, MAC, missingRate, LD_pruning = 0.7, scanThreshold = 1e-2, nperm=100, method="WaldSand")