sartorlab / chipenrich / 57

Builds Branch Commit Type Ran Committer Via Coverage
57 master Rename plot_spline_length.R to plot_chipenrich_spline.R * And the function as well. Clearer. * Added test functions for plot_*() functions. push rcavalcante travis-ci pending completion   set done
56 master Cleanup QC plot functions and add Poly-Enrich QC plot * There was a lot of redundant code in the QC plots. Streamlined to use as much of what had been computed already. * Removed extrandeous fuctions from plot_spline_length.R that were likely lef... push rcavalcante travis-ci pending completion   set done
55 master Cleanup enrich functions and add functions to utils.R * Use simple reset_ncores_for_windows() function instead of repeating logic in each enrich function. * Post-processing of enrichments is the same regardless of tests used, so post_process_enri... push rcavalcante travis-ci pending completion   set done
54 master Clear up multicore logic * Can use parallel::mclapply regardless of platform if mc.cores = 1. * Remove checks in test_*.R functions in favor of forcing n_cores = 1 in *enrich() functions if os = 'Windows'. * Tested on Windows, works fine. * Vigne... push rcavalcante travis-ci pending completion   set done
53 master Remove CHRIS MORE HERE from NEWS :) push rcavalcante travis-ci pending completion   set done
52 master Throw an error for invalid randomization code * Forgot to do this. push rcavalcante travis-ci pending completion   set done
51 master Randomization updates * Include messages at runtime so user realizes they're doing randomizations. * Include a description of the rationale for randomization in the vignette, as well as the options, and what each is telling you. * Bioc packages a... push rcavalcante travis-ci pending completion   set done
50 master Bugfix: Used incorrect peak assignment in chip/polyenrich * In chipenrich() and polyenrich(), was still using assign_peak_segments() after breaking them out. * This shouldn't have affected any runs from Chris and Shuze. push rcavalcante travis-ci pending completion   set done
49 master Vignette improvements push rcavalcante travis-ci pending completion   set done
48 master First draft of revamped vignette * Harmonize with all the recent changes. push rcavalcante travis-ci pending completion   set done
47 master Bugfix: Set default value for randomizations in setup_locusdef() * Should be NULL. push rcavalcante travis-ci pending completion   set done
45 master Breakout polyenrich() * Remove references to polyenrich method in chipenrich(). * Update unit tests and vignette code to prevent errors. * NOTE: Kept method parameter for future method involving weights. * Fixed collision between chipenrich packa... push rcavalcante travis-ci pending completion   set done
44 master Breakout broadenrich() * Remove references to broadenrich method in chipenrich(). * Clear up some of the documentation for both broadenrich() and chipenrich(). It was getting kind of out of date. * Change unit test and vignette code so they run w... push rcavalcante travis-ci pending completion   set done
43 master Streamline preliminary steps in chipenrich() * In preparation for breaking out broadenrich and polyenrich methods into their own functions, we want the internal code in chipenrich() to be as modular as possible. * New setup_locusdef() function is... push rcavalcante travis-ci pending completion   set done
42 master setup_geneset() and setup_ldef() now read_geneset() and read_ldef() * This way we can create setup_*() functions that handle the logic present in chipenrich() so it can be reused in the forthcoming broadenrich() and polyenrich() functions. * Rena... push rcavalcante travis-ci pending completion   set done