coloc.abf

[MoMaz123]

Hi I am running this:

result <- coloc.abf(dataset1=list(pvalues=input$pval_nominalgwas, type="cc", S=0.33, N=5985), dataset2=list(pvalues=input$pval_nominal_eqtl, type="quant",N=7119), MAF=input$maf)

keep having this issues.

result <- coloc.abf(dataset1=list(pvalues=input$pval_nominalgwas, type="cc", S=0.33, N=5985),

•                 dataset2=list(pvalues=input$pval_nominal_eqtl, type="quant",N=7119),MAF=input$maf)
  

Error in check_dataset(d = dataset1, 1) : dataset 1: missing required element(s) snp

Your advise is appreciated.

[chr1swallace]

Each dataset needs a snp identifier. Yours doesn't have one.

-- https://chr1swallace.github.io

---

From: MoMaz123 @.> Sent: Tuesday, September 26, 2023 4:56:38 PM To: chr1swallace/coloc @.> Cc: Subscribed @.***> Subject: [chr1swallace/coloc] coloc.abf (Issue #131)

Hi I am running this:

result <- coloc.abf(dataset1=list(pvalues=input$pval_nominalgwas, type="cc", S=0.33, N=5985), dataset2=list(pvalues=input$pval_nominal_eqtl, type="quant",N=7119), MAF=input$maf)

keep having this issues.

result <- coloc.abf(dataset1=list(pvalues=input$pval_nominalgwas, type="cc", S=0.33, N=5985),

            dataset2=list(pvalues=input$pval_nominal_eqtl, type="quant",N=7119),MAF=input$maf)

Error in check_dataset(d = dataset1, 1) : dataset 1: missing required element(s) snp

Your advise is appreciated.

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