Refactor generate_DEA_reports write_DEA_all and make_SummarizedExperiment into R6 class

[wolski]

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]

move :

prolfquapp/R/run2GrpAnalysis.R

Line 143 in 343523e

make_DEA_report <- function(lfqdata,

and related functions into an R6 class.

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