Created
June 5, 2023 17:55
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Code for performing ASE analysis with DESeq2
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| design <- ~0 + donor + allele | |
| dds <- DESeqDataSetFromMatrix(counts, coldata, design) # counts has the two alleles per donor | |
| assays(dds)[["weights"]] <- weights # 1 for hets, 1e-6 for homs | |
| sizeFactors(dds) <- rep(1, ncol(dds)) | |
| dds <- DESeq(dds, test="LRT", reduced=~0 + donor) | |
| res <- results(dds) |
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