comments.md

In niaid/HDStIM: High Dimensional Stimulation Immune Mapping ('HDStIM')

For Testing

Main HDStIM Function

mapped_data <- HDStIM(chi11$expr_data, chi11$state_markers,
                   chi11$cluster_col, chi11$stim_label,
                   chi11$unstim_label, seed_val = 123, umap = FALSE, umap_cells = NULL,
                   verbose = FALSE)

Marker Ranking by Boruta

attribute_stats <- marker_ranking_boruta(mapped_data, path = NULL, n_cells = NULL,
                                         max_runs = 1000, seed_val = 123,
                                         verbose = FALSE)

For Building

README.Rmd

Changes made to README.Rmd are overwritten on README.md during build. Therefore, do not edit README.md directly. After making changes to README.Rmd run knitr.

Updating Documentation

If the option to update Roxygen2 documentation is enabled in Rstudio settings then it should get triggered by default on package build/install/restart/check. However, if not then use the following command.

devtools::document()

Pkgdown Website

If changes are made to README.Rmd or vignettes, build pkgdown website before pushing the code to GitHub. https://pkgdown.r-lib.org/reference/build_site_github_pages.html.

pkgdown::build_site_github_pages()

Win Builder

devtools::check_win_release()

Check as CRAN

devtools::check(args = c('--as-cran'))
devtools::check(args = c('--as-cran'), env_vars = c(NOT_CRAN = "true", "_R_CHECK_LIMIT_CORES_" = TRUE))

Submit to CRAN

devtools::submit_cran()

niaid/HDStIM documentation built on Oct. 15, 2023, 4:43 p.m.