How do I know the SNPS which are removed when clumping are in a LD block or SNPs not existed in 1000 Genome
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5 weeks ago

Hi everyone, I'm not sure how to know why my SNPs are being removed applying clumping when reading the exposure data (in MR analysis). I would like to know as if the SNPs are being deleted because they're not in 1000 Genome I can use proxies. And this way more IVs will be left for MR analysis. Does anybody take any approaches or we need to do it manually? Any help would be appreciated Paria

Randomization data clumping Mendelian GWAS • 587 views
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Please let us know which program you are using.

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I use TwoSampleMR. And the code is as below:

exp_data <- read_exposure_data("ALS_sig.txt", sep="\t", snp_col= "SNP", beta_col= "b", eaf_col= "effectAlleleFreq", se_col= "StdErr", effect_allele_col= "A1", other_allele_col= "A2", pval_col= "p", samplesize_col= "SampleSize", ncase_col= "N_cases", ncontrol_col= "N_controls", clump=TRUE)

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I see, I am not familiar with this package, unfortunately. Can you not derive the list of excluded SNPs via an indirect process of deduction / elimination? That is, save the list before pruning into a vector, then save the pruned list into another vector, and then determine the differences between both of these.