From c59e3f178d955e0f0ee236d46aa04de3c843ab41 Mon Sep 17 00:00:00 2001 From: Tanushree Tunstall Date: Sat, 27 Feb 2021 10:42:04 +0000 Subject: [PATCH] added adjusted p-values for DM muts comparison --- scripts/ks_test_dr_PS.R | 29 ++++++++++++++++++++++++++++- 1 file changed, 28 insertions(+), 1 deletion(-) diff --git a/scripts/ks_test_dr_PS.R b/scripts/ks_test_dr_PS.R index 759a328..69ca196 100755 --- a/scripts/ks_test_dr_PS.R +++ b/scripts/ks_test_dr_PS.R @@ -264,7 +264,34 @@ rows_to_remove = c("lineage2 vs lineage1", "lineage3 vs lineage1", "lineage3 vs ks_df_combined_f = ks_df_combined[-match(rows_to_remove, ks_df_combined$group),] -#======================================================================= + +#====================== +# P-value adjustments +#======================= +#%% +# add bonferroni adjustment as well +ks_df_combined_f$p_adj_bonferroni = p.adjust(ks_df_combined_f$ks_pvalue, method = "bonferroni") + +ks_df_combined_f$signif_bon = ks_df_combined_f$p_adj_bonferroni +ks_df_combined_f = dplyr::mutate(ks_df_combined_f + , signif_bon = case_when(signif_bon == 0.05 ~ "." + , signif_bon <=0.0001 ~ '****' + , signif_bon <=0.001 ~ '***' + , signif_bon <=0.01 ~ '**' + , signif_bon <0.05 ~ '*' + , TRUE ~ 'ns')) + +#add fdr as well +ks_df_combined_f$p_adj_fdr = p.adjust(ks_df_combined_f$ks_pvalue, method = "hommel") +ks_df_combined_f$signif_fdr = ks_df_combined_f$p_adj_fdr +ks_df_combined_f = dplyr::mutate(ks_df_combined_f + , signif_fdr = case_when(signif_fdr == 0.05 ~ "." + , signif_fdr <=0.0001 ~ '****' + , signif_fdr <=0.001 ~ '***' + , signif_fdr <=0.01 ~ '**' + , signif_fdr <0.05 ~ '*' + , TRUE ~ 'ns')) +#======================================================================================== #****************** # write output file: KS test #******************