I conducted co-localization analysis of eQTL and GWAS using the coloc package with the following code:
result <- coloc.abf(
dataset1 = list(pvalues = input$pval_nominal_gwas, type = "quant", N = 328, snp = input$rs_id, MAF = input$gwas_maf),
dataset2 = list(pvalues = input$pval_nominal_eqtl, type = "quant", N = 666, snp = input$rs_id, MAF = input$maf)
)
I received the following warning messages and would like to know how to address them:
Warning messages:
1: In adjust_prior(p1, nrow(df1), "1") :
p1 nsnps >= 1, setting p1=1/(nsnps + 1)
2: In adjust_prior(p2, nrow(df2), "2") :
p2 nsnps >= 1, setting p2=1/(nsnps + 1)
Could you provide guidance on how to resolve this warning?
I conducted co-localization analysis of eQTL and GWAS using the coloc package with the following code: result <- coloc.abf( dataset1 = list(pvalues = input$pval_nominal_gwas, type = "quant", N = 328, snp = input$rs_id, MAF = input$gwas_maf), dataset2 = list(pvalues = input$pval_nominal_eqtl, type = "quant", N = 666, snp = input$rs_id, MAF = input$maf) ) I received the following warning messages and would like to know how to address them: Warning messages: 1: In adjust_prior(p1, nrow(df1), "1") : p1 nsnps >= 1, setting p1=1/(nsnps + 1) 2: In adjust_prior(p2, nrow(df2), "2") : p2 nsnps >= 1, setting p2=1/(nsnps + 1) Could you provide guidance on how to resolve this warning?