In facileverse/FacileData: A fluent API for accessing multi-assay high-throughput genomics data

library(FacileData)
library(FacileAnalysis)
tcga <- exampleFacileDataSet()

blca <- tcga |> 
  filter_samples(indication == "BLCA") |> 
  with_sample_covariates(c("sample_type", "sex"))

y.blca <- biocbox(blca, class = "DGEList")

DGE

bioc

model <- model.matrix(~ sample_type + sex, data = y.blca$samples)
y <- y.blca[edgeR::filterByExpr(y.blca, model),,keep.lib.sizes = FALSE]
y <- edgeR::calcNormFactors(y)
vm <- limma::voom(y, model)
fit <- limma::lmFit(vm, model)
fit <- limma::eBayes(fit)
res.bioc <- limma::topTable(fit, "sample_typetumor", n = Inf)

model.facile <- blca |> 
  flm_def(covariate = "sample_type", numer = "tumor",
          denom = "normal", batch = "sex")
res.facile <- fdge(model.facile, method = "voom")

res <- iFacileAnalysis::fdgeGadget(blca)

res2 <- iFacileAnalysis::fdgeGadget(tcga)

facileverse/FacileData documentation built on Feb. 24, 2024, 7:59 a.m.