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scripts/parse_hughes_2006.R

@@ -224,59 +224,77 @@ genome_map = tibble(
 
 stopifnot(setequal(genome_map$hughes_target, unique(df_oe$hughes_target)))
 
+hughes_2006_meta_with_id = hughes_2006_meta %>%
+  group_by(regulator_locus_tag) %>%
+  mutate(sample_id = cur_group_id()) %>%
+  ungroup() %>%
+  select(sample_id, all_of(colnames(hughes_2006_meta))) %>%
+  arrange(sample_id)
+
+stopifnot(
+  hughes_2006_meta_with_id %>% group_by(sample_id) %>% filter(n()>1) %>% nrow() == 0
+)
+
 df_oe_harmonized = df_oe %>%
   left_join(
-    select(hughes_2006_meta,
+    select(hughes_2006_meta_with_id,
+           sample_id,
            regulator_locus_tag,
            regulator_symbol)) %>%
   left_join(genome_map) %>%
-  select(regulator_locus_tag, regulator_symbol,
+  select(sample_id,
+         regulator_locus_tag, regulator_symbol,
          target_locus_tag, target_symbol,
          dye_plus, dye_minus, mean_norm_log2fc)
 
-df_oe_harmonized %>%
-  write_parquet("~/code/hf/hughes_2006/overexpression.parquet",
-                compression = "zstd",
-                write_statistics = TRUE,
-                use_dictionary = c(
-                  regulator_locus_tag = TRUE,
-                  regulator_symbol = TRUE,
-                  target_locus_tag = TRUE,
-                  target_symbol = TRUE
-                )
-  )
+# df_oe_harmonized %>%
+#   write_parquet("~/code/hf/hughes_2006/overexpression.parquet",
+#                 compression = "zstd",
+#                 write_statistics = TRUE,
+#                 use_dictionary = c(
+#                   sample_id = TRUE,
+#                   regulator_locus_tag = TRUE,
+#                   regulator_symbol = TRUE,
+#                   target_locus_tag = TRUE,
+#                   target_symbol = TRUE
+#                 )
+#   )
 
 df_ko_harmonized = df_ko %>%
   left_join(
-    select(hughes_2006_meta,
+    select(hughes_2006_meta_with_id,
+           sample_id,
            regulator_locus_tag,
            regulator_symbol)) %>%
   left_join(genome_map) %>%
-  select(regulator_locus_tag, regulator_symbol,
+  select(sample_id,
+         regulator_locus_tag, regulator_symbol,
          target_locus_tag, target_symbol,
          dye_plus, dye_minus, mean_norm_log2fc)
 
-df_ko_harmonized %>%
-  write_parquet("~/code/hf/hughes_2006/knockout.parquet",
-                compression = "zstd",
-                write_statistics = TRUE,
-                use_dictionary = c(
-                  regulator_locus_tag = TRUE,
-                  regulator_symbol = TRUE,
-                  target_locus_tag = TRUE,
-                  target_symbol = TRUE
-                )
-  )
+# df_ko_harmonized %>%
+#   write_parquet("~/code/hf/hughes_2006/knockout.parquet",
+#                 compression = "zstd",
+#                 write_statistics = TRUE,
+#                 use_dictionary = c(
+#                   sample_id = TRUE,
+#                   regulator_locus_tag = TRUE,
+#                   regulator_symbol = TRUE,
+#                   target_locus_tag = TRUE,
+#                   target_symbol = TRUE
+#                 )
+#   )
 
-hughes_2006_meta %>%
-  janitor::clean_names() %>%
-  write_parquet("~/code/hf/hughes_2006/metadata.parquet",
-                compression = "zstd",
-                write_statistics = TRUE,
-                use_dictionary = c(
-                  regulator_locus_tag = TRUE,
-                  regulator_symbol = TRUE,
-                  oe_passed_qc = TRUE,
-                  del_passed_qc = TRUE
-                )
-  )
+# hughes_2006_meta_with_id %>%
+#   janitor::clean_names() %>%
+#   write_parquet("~/code/hf/hughes_2006/metadata.parquet",
+#                 compression = "zstd",
+#                 write_statistics = TRUE,
+#                 use_dictionary = c(
+#                   sample_id = TRUE,
+#                   regulator_locus_tag = TRUE,
+#                   regulator_symbol = TRUE,
+#                   oe_passed_qc = TRUE,
+#                   del_passed_qc = TRUE
+#                 )
+#   )