Compute log2(fold-change) based on the effect size.
add_logfc(results, effect_var = "estimate", force_new = FALSE)The cell type-phenotype enrichment results generated by gen_results and merged together with merge_results
Name of the effect size column in the results.
Force the creation of a new logFC column
even when one already exists.
results = load_example_results()[seq(5000)]
add_logfc(results)
#> Adding logFC column.
#> ctd model_id hpo_id
#> <char> <char> <char>
#> 1: DescartesHuman model10000_35c3c515a8691a HP:0040231
#> 2: DescartesHuman model10000_35c3c517ae4e97 HP:0040231
#> 3: DescartesHuman model10000_35c3c51910bcca HP:0040231
#> 4: DescartesHuman model10000_35c3c5198399fa HP:0040231
#> 5: DescartesHuman model10000_35c3c519a5a6ba HP:0040231
#> ---
#> 4996: DescartesHuman model10059_35d246780870b0 HP:0040416
#> 4997: DescartesHuman model10059_35d24678dd8ec1 HP:0040416
#> 4998: DescartesHuman model10059_35d24679dd709d HP:0040416
#> 4999: DescartesHuman model10059_35d2467b04897e HP:0040416
#> 5000: DescartesHuman model10059_35d2467b79e3c8 HP:0040416
#> CellType term estimate std.error statistic
#> <char> <char> <num> <num> <num>
#> 1: Lymphoid_cells x -0.006377201 0.01435295 -0.4443128
#> 2: Purkinje_neurons x -0.010869399 0.01435240 -0.7573229
#> 3: PDE11A_FAM19A2_positive_cells x -0.006265524 0.01435296 -0.4365317
#> 4: Vascular_endothelial_cells x -0.008501924 0.01435273 -0.5923560
#> 5: Adrenocortical_cells x -0.007390324 0.01435285 -0.5149027
#> ---
#> 4996: Cardiomyocytes x 0.003708823 0.01435315 0.2583979
#> 4997: Acinar_cells x 0.007994311 0.01435279 0.5569867
#> 4998: Stromal_cells x -0.007748407 0.01435281 -0.5398528
#> 4999: ENS_glia x -0.005288765 0.01435304 -0.3684768
#> 5000: Inhibitory_neurons x -0.010224943 0.01435250 -0.7124157
#> p model_p model_q model_estimate model_statistic q
#> <num> <num> <int> <num> <num> <num>
#> 1: 0.6568363 1 1 2.834550e-16 1.975093e-14 0.9999989
#> 2: 0.4488932 1 1 2.834197e-16 1.974924e-14 0.9999989
#> 3: 0.6624704 1 1 2.837708e-16 1.977292e-14 0.9999989
#> 4: 0.5536398 1 1 2.843008e-16 1.981018e-14 0.9999989
#> 5: 0.6066444 1 1 2.842067e-16 1.980345e-14 0.9999989
#> ---
#> 4996: 0.7961108 1 1 1.306766e-16 9.105326e-15 0.9999989
#> 4997: 0.5775622 1 1 1.304462e-16 9.089496e-15 0.9999989
#> 4998: 0.5893233 1 1 1.305320e-16 9.095459e-15 0.9999989
#> 4999: 0.7125338 1 1 1.309416e-16 9.123854e-15 0.9999989
#> 5000: 0.4762416 1 1 1.312929e-16 9.148680e-15 0.9999989
#> annotLevel fold_change logFC
#> <int> <num> <num>
#> 1: 2 0.3823447 -0.4183910
#> 2: 2 0.3659512 -0.8289973
#> 3: 2 0.3827488 -0.4095346
#> 4: 2 0.3746244 -0.5981572
#> 5: 2 0.3786709 -0.5013214
#> ---
#> 4996: 2 0.4182012 0.2195695
#> 4997: 2 0.4330556 0.4235201
#> 4998: 2 0.3773691 -0.5318115
#> 4999: 2 0.3862766 -0.3343068
#> 5000: 2 0.3683196 -0.7624138