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scripts/parse_kemmeren_data.R

@@ -119,9 +119,14 @@ deleteome_all_mutants_controls_long = deleteome_all_mutants_controls %>%
   mutate(kemmeren_regulator = toupper(str_remove(tolower(kemmeren_regulator), "-del-1$|-del-mata$|-del$"))) %>%
   mutate(kemmeren_regulator = ifelse(kemmeren_regulator == "ARG5,6", "ARG56", kemmeren_regulator))
 
-kem_sup1_regulator_info = read_excel(here("data/kemmeren/mmc1.xlsx")) %>%
-  # additional columns are not tabular
-  .[,1:9]
+kem_sup1_regulator_info = read_excel(here("data/kemmeren/supplemental_table1_strain_info.xlsx")) %>%
+  mutate(`profile first published` = str_replace(`profile first published`, ", ", ","))
+kem_sup1_regulator_info_straininfo = read_excel(here("data/kemmeren/supplemental_table1_strain_info_origins.xlsx"))
+
+kem_sup1_regulator_info = kem_sup1_regulator_info %>%
+  left_join(kem_sup1_regulator_info_straininfo) %>%
+  mutate(`profile first published` = citation) %>%
+  select(-citation)
 
 parsed_regulators = deleteome_all_mutants_controls_long %>%
   select(kemmeren_regulator) %>%
@@ -179,7 +184,8 @@ regulators_munging_df = bind_rows(regulators_munging_list) %>%
                     regulator_symbol = symbol)) %>%
   replace_na(list(chase_notes = "none")) %>%
   mutate(regulator_locus_tag = ifelse(str_detect(kemmeren_regulator, "^WT-"), kemmeren_regulator, regulator_locus_tag),
-         regulator_symbol = ifelse(str_detect(kemmeren_regulator, "^WT-"), kemmeren_regulator, regulator_symbol))
+         regulator_symbol = ifelse(str_detect(kemmeren_regulator, "^WT-"), kemmeren_regulator, regulator_symbol)) %>%
+  janitor::clean_names()
 
 
 stopifnot(setequal(regulators_munging_df$kemmeren_regulator,
@@ -251,11 +257,17 @@ final_parsed_df = Reduce(left_join, final_parsed_list) %>%
   # duplicated to mulitple Madj. This removes those duplicates
   distinct(reporterId, .keep_all = TRUE) %>%
   ungroup() %>%
-  left_join(select(regulators_munging_df, kemmeren_regulator,
-                   regulator_locus_tag, regulator_symbol)) %>%
-  select(regulator_locus_tag, regulator_symbol, reporterId,
-         target_locus_tag, target_symbol, M, Madj, A, pval,
-         variable_in_wt, multiple_probes)
+  left_join(select(regulators_munging_df,
+                   -c(gene, `orf_name`))) %>%
+  dplyr::rename(nr_sign_changes = nr_sign_changes_p_0_05_fc_1_7,
+                primary_hybsets = primary_hybset_s,
+                source_of_deletion_mutants = source_of_deletion_mutant_s,
+                slides = slide_s,
+                regulator_desc = description) %>%
+  arrange(regulator_locus_tag)
+  # select(regulator_locus_tag, regulator_symbol, reporterId,
+  #        target_locus_tag, target_symbol, M, Madj, A, pval,
+  #        variable_in_wt, multiple_probes)
 
 db_kemmeren_meta = read_csv("data/kemmeren/db_kemmeren_meta_20251126.csv") %>%
   mutate(id = ifelse(regulator_locus_tag == 'YLR352W', 0, id)) %>%
@@ -270,11 +282,11 @@ final_df_parsed_with_ids = final_parsed_df %>%
   arrange(regulator_locus_tag) %>%
   group_by(regulator_locus_tag) %>%
   mutate(sample_id = cur_group_id()) %>%
-  select(sample_id,db_id,
-         regulator_locus_tag,regulator_symbol,reporterId,
-         target_locus_tag,target_symbol,
-         M,Madj,A,pval,
-         variable_in_wt,multiple_probes)
+  relocate(sample_id, db_id,
+           regulator_locus_tag, regulator_symbol,
+           reporterId, target_locus_tag, target_symbol,
+           M, Madj, A, pval,
+           variable_in_wt, multiple_probes)
 
 # note! verify before overwriting that the sample_id for the unique sample
 # tuple is the same as it is in the current hackett_2020, or that any changes
@@ -290,4 +302,3 @@ final_df_parsed_with_ids = final_parsed_df %>%
 #                   target_locus_tag = TRUE
 #                 )
 #   )
-