[WIP] Helper function to remove batch effects#280
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hertafeldsr wants to merge 10 commits intov1.6rcfrom
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[WIP] Helper function to remove batch effects#280hertafeldsr wants to merge 10 commits intov1.6rcfrom
hertafeldsr wants to merge 10 commits intov1.6rcfrom
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hertafeldsr
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daler
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May 9, 2020
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Thanks -- small review comments below
| beta <- fit$coefficients[,-(1:ncol(design)),drop=FALSE] | ||
| beta[is.na(beta)] <- 0 | ||
| as.matrix(x) - beta %*% t(X.batch) | ||
| } |
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I think this would benefit from a small test -- we wouldn't need to mock up a bunch of RNA-seq data for this, we could just use a small matrix.
And maybe as a temporary test you could copy the function over to a real-world RNA-seq analysis and give it a shot there -- no need to wait for a merge for that.
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@hertafeldsr in 6095688 I added a test Rmd you can use for trying out the function. We may need to find another Bioconductor package with a more complex design in order to test multiple batches. |
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This is for issue #255 . I refactored the code from this function: https://rdrr.io/bioc/limma/src/R/removeBatchEffect.R to be able to accept an arbitrary number of factors. I haven't tested it much yet so I'll have to wait to merge until that's done.