umr1283 / reffreeewas

EWAS using Reference-Free DNA Methylation Mixture Deconvolution

UMR 1283 - Project Template

You can install umr1283 with:

remotes::install_github("umr1283/umr1283")

The default project directory architecture from umr1283::create_project (compatible with RStudio Project Wizard) is as follow:

library(umr1283)
create_project(path = "my-project", analyst_name = "UMR1283")

tree -a my-project
#> my-project/
#> ├── data
#> ├── .devcontainer
#> │   ├── devcontainer.json
#> │   └── Dockerfile
#> ├── docs
#> ├── .gitignore
#> ├── logs
#> ├── my-project.Rproj
#> ├── outputs
#> ├── README.md
#> ├── renv
#> ├── reports
#> ├── .Rprofile
#> ├── scripts
#> │   ├── 00-targets.R
#> │   ├── _dependencies.R
#> │   └── tar-utils
#> ├── _targets
#> └── _targets.R
#> 
#> 10 directories, 9 files

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Getting help

If you encounter a clear bug, please file a minimal reproducible example on GitHub.
For questions and other discussion, please open a discussion on GitHub.

reffreeewas's Issues

Allows `future` framework for bootstrap functions

• Replace with future.apply::future_replicate (must check default simplify = "array")

  RefFreeEWAS/R/BootRefFreeEwasModel.R

  Line 36 in 2780768

  BetaBoot <- replicate(

• Refactor PairsBootRefFreeEwasModel

  RefFreeEWAS/R/PairsBootRefFreeEwasModel.R

  Lines 33 to 58 in 2780768

  	PairsBootRefFreeEwasModel <- function(mod, nboot, pairID) {
  	BetaBoot <- array(NA, dim = c(dim(mod$Beta), 2, nboot))
  	dimnames(BetaBoot)[1:2] <- dimnames(mod$Beta)
  	dimnames(BetaBoot)[[3]] <- c("B", "B*")
  	dimnames(BetaBoot)[[4]] <- 1:nboot
  	attr(BetaBoot, "nSample") <- dim(mod$X)[1]
  	for (r in 1:nboot) {
  	isError <- TRUE
  	while (isError) {
  	catchError <- try({
  	Yboot <- PairsBootOneRefFreeEwasModel(mod, pairID)
  	bootFit <- RefFreeEwasModel(Yboot, mod$X, dim(mod$Lambda)[2],
  	smallOutput = TRUE
  	)
  	BetaBoot[, , 1, r] <- bootFit$Beta
  	BetaBoot[, , 2, r] <- bootFit$Bstar
  	})
  	isError <- inherits(catchError, "try-error")
  	}
  	if (r %% 10 == 0) {
  	cat(r, "\n")
  	}
  	}
  	class(BetaBoot) <- "BootRefFreeEwasModel"
  	BetaBoot
  	}