Create a makefile that runs the whole analysis from scratch

[neurogenomics]

Create a makefile that runs the whole analysis from scratch

[bobGSmith]

I have sorted out the generate results script so that it just calls the gen_results function from MultiEWCE. I'm fairly confident that it would work well on other cases of multiple gene list EWCE. Just need to figure out how to do the vignettes for the package and then unit tests.

## Load data ##################################################################
phenotype_to_genes <- HPOExplorer::load_phenotype_to_genes("data/phenotype_to_genes.txt")
ctd <- readRDS("data/CTD_Descartes_withplot.rds")

## Run analysis ################################################################
all_results <- MultiEWCE::gen_results(ctd,
                                      phenotype_to_genes,
                                      list_names = unique(phenotype_to_genes$Phenotype),
                                      background_genes = unique(phenotype_to_genes$Gene),
                                      list_name_column = "Phenotype",
                                      gene_column = "Gene",
                                      results_dir = "results_test_191021",
                                      overwrite_past_analysis = FALSE,
                                      reps = 100000,
                                      annotLevel = 1,
                                      genelistSpecies = "human",
                                      cores = 8,
                                      MergeResults = TRUE)

## Save merged results ##########################################################
saveRDS(all_results, paste0("HPO_EWCE_Results ",stringr::str_replace_all(Sys.time(),":",""),".rds"))

[bobGSmith]

@NathanSkene I made a dev branch and added a directory called Makefile, which contains:

1. Makefile.R
2. Writeup.Rmd - the markdown template for the report.
3. source/ - contains the code needed to run all the steps end to end (create the CTD, generate results and then pass the results to the markdown and knit it).

The only problem is, I haven't been able to test the final step as I don't have a complete set of results and the Writeup.Rmd is expecting a lot of cardiac terms. I almost got it to work by swapping everything to bladder related terms but a few parts still tripped up.

[bschilder]

Awesome work @ovrhuman! Once it's ready, I can help take a look over it and make edits/suggestions as needed

[NathanSkene]

Looks much more like what we need! Is it clear enough how to setup the vignette and unit tests?

[bobGSmith]

@bschilder Nice thanks that would be really helpful!
@NathanSkene Thanks, yeah I'm going to use the "Making your first R package" guide you sent me. I think I have an idea of what it will cover. I don't have a lot of ideas for unit tests yet but i'm imagining that I will come up with more once I start making them.