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prolfqua / prolfquapp

Generating Dynamic DEA Reports with the prolfqua R Package
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Refactor generate_DEA_reports write_DEA_all and make_SummarizedExperiment into R6 class #11

Open wolski opened 5 months ago

wolski commented 5 months ago

Review the functions since. Maybe move make_SummarizedExperiment into write_DEA_all? Or use the R6 class to minimize the number of parameters.

logger::log_info("run analysis")
grp <- prolfquapp::generate_DEA_reports2(lfqdata, GRP2, xd$protein_annotation, annotation$contrasts)

logger::log_info("write results and html reports")
prolfquapp::write_DEA_all(grp[[1]], names(grp)[1], GRP2$zipdir , boxplot = FALSE, markdown = "_Grp2Analysis_V2.Rmd")

logger::log_info("write results and summarized experiment")
SE <- prolfquapp::make_SummarizedExperiment(grp[[1]])

saveRDS(SE, file = file.path(GRP2$zipdir,
                             paste0("DE_", names(grp)[1], "_WU", grp[[1]]$project_spec$workunitID) ,
                             paste0("SummarizedExperiment",".rds") ))
wolski commented 4 months ago

move : https://github.com/prolfqua/prolfquapp/blob/343523e058ae7ded1336655a6e23b245acda0bb9/R/run2GrpAnalysis.R#L143 and related functions into an R6 class.

This is needed so functionality like generating iBAQ values can be added.