Hello everyone, I have genotype file and gene expression file. I want to see whether three of my rsid in genotype file is associated with gene expression. I used matrixeqtl R package to generate p value and see whether the selected snp is associated with the gene expression. I used this code:
me = Matrix_eQTL_engine( snps = snps, gene = gene, cvrt = cvrt, output_file_name = output_file_name, pvOutputThreshold = pvOutputThreshold, useModel = useModel, errorCovariance = errorCovariance, verbose = TRUE, pvalue.hist = TRUE, min.pv.by.genesnp = FALSE, noFDRsaveMemory = FALSE) unlink(output_file_name) show(me$all$eqtls) output: Processing covariates Task finished in 0.004 seconds Processing gene expression data (imputation, residualization) Task finished in 0.004 seconds Creating output file(s) Task finished in 0.022 seconds Performing eQTL analysis 100.00% done, 0 eQTLs No significant associations were found.
I looked at the snps and they have effect for this gene in gtex models but during matrixeqtl analysis it doesn't show any association.
I don't want to focus on eqtl but rather just generate pvalue and associated z score for the snp-gene pair. Is there any software or tool to do that?