Man pages for lefeverde/QSPpaper
Analysis notebooks and functions for NAFLD QSP paper
| add_p_vals_to_cmap_para | Same as 'add_p_vals_to_cmap_single' but parallel |
| add_p_vals_to_cmap_single | Calculates p-values for CMap results |
| best_score_mat | Chooses the best score per compound |
| best_score_top20 | Returns the top 20 compounds using the best score approach |
| broad_cmap_score | Calculates CMAP score using the Broad's latest methodology... |
| calculate_ncs | Normalizes the connectivity score by cell type |
| calculate_pert_cell_score | Calculates pert score per cell type |
| calculate_pert_score | Calculates the perturbagen summary score |
| chunker | Splits a vector into chunks |
| create_annot_leg_params | Creates legend paramaters for 'HeatmapAnnotation' |
| create_gsea_plot_data | Creates a data.frame to make a GSEA plot |
| create_heatmap_leg_params | Creates legend paramaters for 'Heatmap' |
| gctx_to_sigList | Converts GCTX file to list signature list |
| get_random_cmap_scores | Runs the permutation testing to get a vector of CMAP scores |
| kegg_gsea_by_coef | Wrapper to do GSEA on tidy results |
| lincs2017_score_top20 | Returns the top 20 compounds after performing maximum... |
| make_cont_fit | Wrapper to create a fit object (see 'eBayes') using the... |
| make_gsea_plot | Creates a running sum GSEA plot |
| make_permute_sort_df | Internal function to create a data.frame with the ordered... |
| multi_broad_wrapper | Wrapper to run the 'broad_cmap_score' for many gene sets |
| single_broad_wrapper | Wrapper to run the 'broad_cmap_score' for a single gene set |
| uniquefy_res_by_group | Uniquefys a res df by group by taking absolute max |
