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Removing chrX and chrY probes

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epzjlm edited this page Apr 4, 2018 · 3 revisions 
meffil.list.featuresets()
featureset<-"450k"
autosomal.sites <- meffil.get.autosomal.sites(featureset)
autosomal.sites <- intersect(autosomal.sites, rownames(norm.beta))
norm.beta <- norm.beta[autosomal.sites,]
  1. Installation
  2. Sample QC
  3. Functional normalization
  4. Functional normalizing separate datasets
  5. Extracting structural variants
  6. Estimating cellular composition
  7. Removing chrX and chrY probes
  8. Running EWAS
  9. Extracting CpG annotations
  10. Extracting SNP annotations
  11. Extracting detection p-values
  12. Extracting methylated and unmethylated intensities
  13. Generate normalization report from normalised betas
  14. Full pipeline for analysing massive datasets
  15. Common problems
  16. Citation
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