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I have data that looks like this: 3 column SNPs their gene based on Annovar and a p-value for every SNP. What I would like is to aggregate the p values for every gene.

snps <- data.frame(
  snp_id = c("rs1", "rs2", "rs3", "rs4", "rs5", "rs6", "rs7", "rs8"),
  Gene.refGene_ANNOVAR = c("gene1", "gene1", "gene1", "gene1", "gene2", "gene2", "gene2", "gene2"),
  p.value = c(0.7703884, 0.9648540, 0.9648540, 0.9648540, 0.54, 0.03, 0.03, 0.8)
)

above an example of the data . I read about the SKAT method -> https://www.hsph.harvard.edu/skat/
and figured it might do the work . I read about the package here:https://rdrr.io/cran/SKAT/man/SKAT.html tried to implement it on my data , but got lost as how to perform it correctly:

gene_pvals <- aggregate(p.value ~ Gene.refGene_ANNOVAR, data = df, FUN = function(x) SKAT::SKAT_Null(x)$p.value)

I would be happy if you could share your knowledge in this situation.I don't have information about the correlations between the SNPs but I know that they are correlated, do I have enough data to complete the SKAT method? also for every SNP i have data on how many patients had the hetro/homozygous encoding(0,1,2).

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  • $\begingroup$ cross posted: biostars.org/p/9558525 $\endgroup$
    – Pierre
    Mar 24, 2023 at 15:48
  • $\begingroup$ Unfortunately i didn't recive any helpful reply in BIOSTARS would be happy for help here $\endgroup$
    – liza
    Apr 1, 2023 at 10:32

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