hammerlab / cohorts

Utilities for analyzing mutations and neoepitopes in patient cohorts
Apache License 2.0
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Add `batch` identifier to cohorts & support estimation of batch effects #160

Open jburos opened 7 years ago

jburos commented 7 years ago

Would be useful to keep track of batch identifiers so we can estimate batch effects as part of standard protocol.

jburos commented 7 years ago

Two parts to this request:

  1. [ ] add batch to sample meta-data
  2. [ ] implement method for summarizing batch effects, depending on type of sample

Possible methods for detecting batch effects:

  1. run combat on our samples to estimate batch effects from RNA-seq
  2. use SVA to try to estimate batch effects
  3. look for hierarchical clustering in DNA/RNA more generally